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1. Newly Identified Mycobacterium africanum Lineage 10, Central Africa

Author

Christophe Guyeux, Gaetan Senelle, Adrien Le Meur, Philip Supply, Cyril Gaudin, Jody E. Phelan, Taane G Clark, Leen Rigouts, Bouke de Jong, Christophe Sola, and Guislaine Refrégier

Subjects
Mycobacterium tuberculosis, tuberculosis and other mycobacteria, TB, respiratory infections, bacteria, pathogen diversification, Medicine, Infectious and parasitic diseases, RC109-216
Abstract

Analysis of genome sequencing data from >100,000 genomes of Mycobacterium tuberculosis complex using TB-Annotator software revealed a previously unknown lineage, proposed name L10, in central Africa. Phylogenetic reconstruction suggests L10 could represent a missing link in the evolutionary and geographic migration histories of M. africanum.

Published
2024
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2. A smooth tubercle bacillus from Ethiopia phylogenetically close to the Mycobacterium tuberculosis complex

Author

Bazezew Yenew, Arash Ghodousi, Getu Diriba, Ephrem Tesfaye, Andrea Maurizio Cabibbe, Misikir Amare, Shewki Moga, Ayinalem Alemu, Binyam Dagne, Waganeh Sinshaw, Hilina Mollalign, Abyot Meaza, Mengistu Tadesse, Dinka Fikadu Gamtesa, Yeshiwork Abebaw, Getachew Seid, Betselot Zerihun, Melak Getu, Matteo Chiacchiaretta, Cyril Gaudin, Michael Marceau, Xavier Didelot, Getachew Tolera, Saro Abdella, Abebaw Kebede, Muluwork Getahun, Zemedu Mehammed, Philip Supply, and Daniela Maria Cirillo

Subjects
Science
Abstract

Abstract The Mycobacterium tuberculosis complex (MTBC) includes several human- and animal-adapted pathogens. It is thought to have originated in East Africa from a recombinogenic Mycobacterium canettii-like ancestral pool. Here, we describe the discovery of a clinical tuberculosis strain isolated in Ethiopia that shares archetypal phenotypic and genomic features of M. canettii strains, but represents a phylogenetic branch much closer to the MTBC clade than to the M. canettii strains. Analysis of genomic traces of horizontal gene transfer in this isolate and previously identified M. canettii strains indicates a persistent albeit decreased recombinogenic lifestyle near the emergence of the MTBC. Our findings support that the MTBC emergence from its putative free-living M. canettii-like progenitor is evolutionarily very recent, and suggest the existence of a continuum of further extant derivatives from ancestral stages, close to the root of the MTBC, along the Great Rift Valley.

Published
2023
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3. Transcontinental spread and evolution of Mycobacterium tuberculosis W148 European/Russian clade toward extensively drug resistant tuberculosis

Author

Matthias Merker, Jean-Philippe Rasigade, Maxime Barbier, Helen Cox, Silke Feuerriegel, Thomas A. Kohl, Egor Shitikov, Kadri Klaos, Cyril Gaudin, Rudy Antoine, Roland Diel, Sonia Borrell, Sebastien Gagneux, Vladyslav Nikolayevskyy, Sönke Andres, Valeriu Crudu, Philip Supply, Stefan Niemann, and Thierry Wirth

Subjects
Science
Abstract

An outbreak of the multidrug-resistant Mycobacterium tuberculosis lineage W148 has spread widely across Russia, Central Asia and Europe. Here, the authors use whole genome sequences of ~700 isolates of this lineage collected over ~20 years to analyze its spread, evolution of drug resistance, and impact of compensatory mutations.

Published
2022
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4. Hi-plex deep amplicon sequencing for identification, high-resolution genotyping and multidrug resistance prediction of Mycobacterium leprae directly from patient biopsies by using Deeplex Myc-LepResearch in context

Author

Agathe Jouet, Sofie Marijke Braet, Cyril Gaudin, Gaëlle Bisch, Sidra Vasconcellos, Rebecca Emmanuela Epaminondas Nicacio de Oliveira do Livramento, Yrneh Yadamis Prado Palacios, Amanda Brum Fontes, Norma Lucena, Patricia Rosa, Milton Moraes, Kevin La, Nelly Badalato, Esteban Lenoir, Alice Ferré, Marie Clément, Epco Hasker, Silahi Halifa Grillone, Wirdane Abdou, Aouladi Said, Younoussa Assoumani, Nissad Attoumani, Yannick Laurent, Emmanuelle Cambau, Bouke Catherine de Jong, Philip Noël Suffys, and Philip Supply

Subjects
Mycobacterium leprae, Targeted next generation sequencing, Antibiotic resistance, Gene domain duplication, Diagnostics, Surveillance, Medicine, Medicine (General), R5-920
Abstract

Summary: Background: Expansion of antimicrobial resistance monitoring and epidemiological surveillance are key components of the WHO strategy towards zero leprosy. The inability to grow Mycobacterium leprae in vitro precludes routine phenotypic drug susceptibility testing, and only limited molecular tests are available. We evaluated a culture-free targeted deep sequencing assay, for mycobacterial identification, genotyping based on 18 canonical SNPs and 11 core variable-number tandem-repeat (VNTR) markers, and detection of rifampicin, dapsone and fluoroquinolone resistance-associated mutations in rpoB/ctpC/ctpI, folP1, gyrA/gyrB, respectively, and hypermutation-associated mutations in nth. Methods: The limit of detection (LOD) was determined using DNA of M. leprae reference strains and from 246 skin biopsies and 74 slit skin smears of leprosy patients, with genome copies quantified by RLEP qPCR. Sequencing results were evaluated versus whole genome sequencing (WGS) data of 14 strains, and versus VNTR-fragment length analysis (FLA) results of 89 clinical specimens. Findings: The LOD for sequencing success ranged between 80 and 3000 genome copies, depending on the sample type. The LOD for minority variants was 10%. All SNPs detected in targets by WGS were identified except in a clinical sample where WGS revealed two dapsone resistance-conferring mutations instead of one by Deeplex Myc-Lep, due to partial duplication of the sulfamide-binding domain in folP1. SNPs detected uniquely by Deeplex Myc-Lep were missed by WGS due to insufficient coverage. Concordance with VNTR-FLA results was 99.4% (926/932 alleles). Interpretation: Deeplex Myc-Lep may help improve the diagnosis and surveillance of leprosy. Gene domain duplication is an original putative drug resistance-related genetic adaptation in M. leprae. Funding: EDCTP2 programme supported by the European Union (grant number RIA2017NIM-1847 -PEOPLE). EDCTP, R2Stop: Effect:Hope, The Mission To End Leprosy, the Flemish Fonds Wetenschappelijk Onderzoek.

Published
2023
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5. Updating the WHO target product profile for next-generation Mycobacterium tuberculosis drug susceptibility testing at peripheral centres.

Author

Emily Lai-Ho MacLean, Paolo Miotto, Lice González Angulo, Matteo Chiacchiaretta, Timothy M Walker, Martina Casenghi, Camilla Rodrigues, Timothy C Rodwell, Philip Supply, Emmanuel André, Mikashmi Kohli, Morten Ruhwald, Daniela Maria Cirillo, Nazir Ismail, and Matteo Zignol

Subjects
Public aspects of medicine, RA1-1270
Abstract

There were approximately 10 million tuberculosis (TB) cases in 2020, of which 500,000 were drug-resistant. Only one third of drug-resistant TB cases were diagnosed and enrolled on appropriate treatment, an issue partly driven by a lack of rapid, accurate drug-susceptibility testing (DST) tools deployable in peripheral settings. In 2014, World Health Organization (WHO) published target product profiles (TPPs) which detailed minimal and optimal criteria to address high-priority TB diagnostic needs, including DST. Since then, the TB community's needs have evolved; new treatment regimens, changes in TB definitions, further emergence of drug resistance, technological advances, and changing end-users requirements have necessitated an update. The DST TPP's revision was therefore undertaken by WHO with the Stop TB Partnership New Diagnostics Working Group. We describe the process of updating the TPP for next-generation TB DST for use at peripheral centres, highlight key updates, and discuss guidance regarding technical and operational specifications.

Published
2023
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6. A sister lineage of the Mycobacterium tuberculosis complex discovered in the African Great Lakes region

Author

Jean Claude Semuto Ngabonziza, Chloé Loiseau, Michael Marceau, Agathe Jouet, Fabrizio Menardo, Oren Tzfadia, Rudy Antoine, Esdras Belamo Niyigena, Wim Mulders, Kristina Fissette, Maren Diels, Cyril Gaudin, Stéphanie Duthoy, Willy Ssengooba, Emmanuel André, Michel K. Kaswa, Yves Mucyo Habimana, Daniela Brites, Dissou Affolabi, Jean Baptiste Mazarati, Bouke Catherine de Jong, Leen Rigouts, Sebastien Gagneux, Conor Joseph Meehan, and Philip Supply

Subjects
Science
Abstract

The human- and animal-adapted lineages of the Mycobacterium tuberculosis complex (MTBC) are thought to be evolved from a common progenitor in Africa. Here, the authors identify two MTBC strains isolated from patients with multidrug-resistant tuberculosis, representing an as-yet-unknown lineage further supporting an East African origin for the MTBC.

Published
2020
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7. The 2021 WHO catalogue of Mycobacterium tuberculosis complex mutations associated with drug resistance: a genotypic analysis

Author

Timothy M Walker, DPhil, Paolo Miotto, PhD, Claudio U Köser, PhD, Philip W Fowler, PhD, Jeff Knaggs, BSc, Zamin Iqbal, DPhil, Martin Hunt, PhD, Leonid Chindelevitch, PhD, Maha R Farhat, MD, Daniela Maria Cirillo, PhD, Iñaki Comas, PhD, James Posey, PhD, Shaheed V Omar, PhD, Timothy EA Peto, ProfFRCP, Anita Suresh, MSc, Swapna Uplekar, PhD, Sacha Laurent, PhD, Rebecca E Colman, PhD, Carl-Michael Nathanson, PhD, Matteo Zignol, MD, Ann Sarah Walker, ProfPhD, Derrick W Crook, ProfFRCPath, Nazir Ismail, FRCPath [SA], Timothy C Rodwell, ProfMD, A Sarah Walker, Adrie J C Steyn, Ajit Lalvani, Alain Baulard, Alan Christoffels, Alberto Mendoza-Ticona, Alberto Trovato, Alena Skrahina, Alexander S Lachapelle, Alice Brankin, Amy Piatek, Ana Gibertoni Cruz, Anastasia Koch, Andrea Maurizio Cabibbe, Andrea Spitaleri, Angela P Brandao, Angkana Chaiprasert, Anita Suresh, Anna Barbova, Annelies Van Rie, Arash Ghodousi, Arnold Bainomugisa, Ayan Mandal, Aysha Roohi, Babak Javid, Baoli Zhu, Brice Letcher, Camilla Rodrigues, Camus Nimmo, Carl-Michael NATHANSON, Carla Duncan, Christopher Coulter, Christian Utpatel, Chunfa Liu, Clara Grazian, Clare Kong, Claudio U Köser, Daniel J Wilson, Daniela Maria Cirillo, Daniela Matias, Danielle Jorgensen, Danila Zimenkov, Darren Chetty, David AJ Moore, David A Clifton, Derrick W Crook, Dick van Soolingen, Dongxin Liu, Donna Kohlerschmidt, Draurio Barreira, Dumisani Ngcamu, Elias David Santos Lazaro, Ellis Kelly, Emanuele Borroni, Emma Roycroft, Emmanuel Andre, Erik C Böttger, Esther Robinson, Fabrizio Menardo, Flavia F Mendes, Frances B Jamieson, Francesc Coll, George Fu Gao, George W Kasule, Gian Maria Rossolini, Gillian Rodger, E Grace Smith, Graeme Meintjes, Guy Thwaites, Harald Hoffmann, Heidi Albert, Helen Cox, Ian F Laurenson, Iñaki Comas, Irena Arandjelovic, Ivan Barilar, Jaime Robledo, James Millard, James Johnston, Jamie Posey, Jason R Andrews, Jeff Knaggs, Jennifer Gardy, Jennifer Guthrie, Jill Taylor, Jim Werngren, John Metcalfe, Jorge Coronel, Joseph Shea, Joshua Carter, Juliana MW Pinhata, Julianne V Kus, Katharina Todt, Kathryn Holt, Kayzad S Nilgiriwala, Kelen T Ghisi, Kerri M Malone, Kiatichai Faksri, Kimberlee A Musser, Lavania Joseph, Leen Rigouts, Leonid Chindelevitch, Lisa Jarrett, Louis Grandjean, Lucilaine Ferrazoli, Mabel Rodrigues, Maha Farhat, Marco Schito, Margaret M Fitzgibbon, Marguerite Massinga Loembé, Maria Wijkander, Marie Ballif, Marie-Sylvianne Rabodoarivelo, Marina Mihalic, Mark WILCOX, Martin Hunt, Matteo ZIGNOL, Matthias Merker, Matthias Egger, Max O'Donnell, Maxine Caws, Mei-Hua Wu, Michael G Whitfield, Michael Inouye, Mikael Mansjö, Minh Ha Dang Thi, Moses Joloba, SM Mostofa Kamal, Nana Okozi, Nazir ISMAIL, Nerges Mistry, Nhung N Hoang, Niaina Rakotosamimanana, Nicholas I Paton, Paola M V Rancoita, Paolo Miotto, Pascal Lapierre, Patricia J Hall, Patrick Tang, Pauline Claxton, Penelope Wintringer, Peter M Keller, Phan Vuong Khac Thai, Philip W Fowler, Philip Supply, Prapaporn Srilohasin, Prapat Suriyaphol, Priti Rathod, Priti Kambli, Ramona Groenheit, Rebecca E Colman, Rick Twee-Hee Ong, Robin M Warren, Robert J Wilkinson, Roland Diel, Rosangela S Oliveira, Rukhsar Khot, Ruwen Jou, Sabira Tahseen, Sacha Laurent, Saheer Gharbia, Samaneh Kouchaki, Sanchi Shah, Sara Plesnik, Sarah G Earle, Sarah Dunstan, Sarah J Hoosdally, Satoshi Mitarai, Sebastien Gagneux, Shaheed V Omar, Shen-Yuan Yao, Simon Grandjean Lapierre, Simone Battaglia, Stefan Niemann, Sushil Pandey, Swapna Uplekar, Tanya A Halse, Ted Cohen, Teresa Cortes, Therdsak Prammananan, Thomas A Kohl, Nguyen T T Thuong, Tik Ying Teo, Timothy E A Peto, Timothy C Rodwell, Timothy William, Timothy M Walker, Thomas R Rogers, Utkarsha Surve, Vanessa Mathys, Victoria Furió, Victoria Cook, Srinivasan Vijay, Vincent Escuyer, Viola Dreyer, Vitali Sintchenko, Vonthanak Saphonn, Walter Solano, Wan-Hsuan Lin, Wayne van Gemert, Wencong He, Yang Yang, Yanlin Zhao, Youwen Qin, Yu-Xin Xiao, Zahra Hasan, Zamin Iqbal, and Zully M Puyen

Subjects
Medicine (General), R5-920, Microbiology, QR1-502
Abstract

Summary: Background: Molecular diagnostics are considered the most promising route to achievement of rapid, universal drug susceptibility testing for Mycobacterium tuberculosis complex (MTBC). We aimed to generate a WHO-endorsed catalogue of mutations to serve as a global standard for interpreting molecular information for drug resistance prediction. Methods: In this systematic analysis, we used a candidate gene approach to identify mutations associated with resistance or consistent with susceptibility for 13 WHO-endorsed antituberculosis drugs. We collected existing worldwide MTBC whole-genome sequencing data and phenotypic data from academic groups and consortia, reference laboratories, public health organisations, and published literature. We categorised phenotypes as follows: methods and critical concentrations currently endorsed by WHO (category 1); critical concentrations previously endorsed by WHO for those methods (category 2); methods or critical concentrations not currently endorsed by WHO (category 3). For each mutation, we used a contingency table of binary phenotypes and presence or absence of the mutation to compute positive predictive value, and we used Fisher's exact tests to generate odds ratios and Benjamini-Hochberg corrected p values. Mutations were graded as associated with resistance if present in at least five isolates, if the odds ratio was more than 1 with a statistically significant corrected p value, and if the lower bound of the 95% CI on the positive predictive value for phenotypic resistance was greater than 25%. A series of expert rules were applied for final confidence grading of each mutation. Findings: We analysed 41 137 MTBC isolates with phenotypic and whole-genome sequencing data from 45 countries. 38 215 MTBC isolates passed quality control steps and were included in the final analysis. 15 667 associations were computed for 13 211 unique mutations linked to one or more drugs. 1149 (7·3%) of 15 667 mutations were classified as associated with phenotypic resistance and 107 (0·7%) were deemed consistent with susceptibility. For rifampicin, isoniazid, ethambutol, fluoroquinolones, and streptomycin, the mutations' pooled sensitivity was more than 80%. Specificity was over 95% for all drugs except ethionamide (91·4%), moxifloxacin (91·6%) and ethambutol (93·3%). Only two resistance mutations were identified for bedaquiline, delamanid, clofazimine, and linezolid as prevalence of phenotypic resistance was low for these drugs. Interpretation: We present the first WHO-endorsed catalogue of molecular targets for MTBC drug susceptibility testing, which is intended to provide a global standard for resistance interpretation. The existence of this catalogue should encourage the implementation of molecular diagnostics by national tuberculosis programmes. Funding: Unitaid, Wellcome Trust, UK Medical Research Council, and Bill and Melinda Gates Foundation.

Published
2022
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8. Drug-Resistant Tuberculosis, Lebanon, 2016 – 2017

Author

Salam El Achkar, Christine Demanche, Marwan Osman, Rayane Rafei, Mohamad Bachar Ismail, Hiam Yaacoub, Claire Pinçon, Stéphanie Duthoy, Frédérique De Matos, Cyril Gaudin, Alberto Trovato, Daniela M. Cirillo, Monzer Hamze, and Philip Supply

Subjects
Tuberculosis, TB, MDR, XDR, drug resistance, survey, Medicine, Infectious and parasitic diseases, RC109-216
Abstract

In a 12-month nationwide study on the prevalence of drug-resistant tuberculosis (TB) in Lebanon, we identified 3 multidrug-resistant cases and 3 extensively drug-resistant TB cases in refugees, migrants, and 1 Lebanon resident. Enhanced diagnostics, particularly in major destinations for refugees, asylum seekers, and migrant workers, can inform treatment decisions and may help prevent the spread of drug-resistant TB.

Published
2019
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9. Prevalence and drivers of false-positive rifampicin-resistant Xpert MTB/RIF results: a prospective observational study in Rwanda

Author

Jean Claude Semuto Ngabonziza, MSc, Tom Decroo, PhD, Patrick Migambi, MSc, Yves Mucyo Habimana, MD, Armand Van Deun, PhD, Conor J Meehan, PhD, Gabriela Torrea, PhD, Faridath Massou, PharmD, Willem Bram de Rijk, BS, Bertin Ushizimpumu, BS, Esdras Belamo Niyigena, BS, Emil Ivan, PhD, Jules Mugabo Semahore, MD, Jean Baptiste Mazarati, PhD, Corinne Simone Merle, PhD, Philip Supply, PhD, Dissou Affolabi, ProfPhD, Leen Rigouts, PhD, and Bouke Catherine de Jong, ProfPhD

Subjects
Medicine (General), R5-920, Microbiology, QR1-502
Abstract

Summary: Background: The Xpert MTB/RIF (Xpert) assay is used globally to rapidly diagnose tuberculosis and resistance to rifampicin. We investigated the frequency and predictors of false-positive findings of rifampicin resistance with Xpert. Methods: We did a prospective, observational study of individuals who were enrolled in a Rwandan nationwide diagnostic cohort study (DIAMA trial; NCT03303963). We included patients identified to have rifampicin resistance on initial Xpert testing. We did a repeat Xpert assay and used rpoB Sanger and deep sequencing alongside phenotypic drug susceptibility testing (pDST) to ascertain final rifampicin susceptibility status, with any (hetero)resistant result overriding. We used multivariable logistic regression to assess predictors of false rifampicin resistance on initial Xpert testing, adjusted for HIV status, tuberculosis treatment history, initial Xpert semi-quantitative bacillary load, and initial Xpert probe. Findings: Between May 4, 2017, and April 30, 2019, 175 people were identified with rifampicin resistance at initial Xpert testing, of whom 154 (88%) underwent repeat Xpert assay. 54 (35%) patients were confirmed as rifampicin resistant on repeat testing and 100 (65%) were not confirmed with resistance. After further testing and sequencing, 121 (79%) of 154 patients had a final confirmed status for rifampicin susceptibility. 57 (47%) of 121 patients were confirmed to have a false rifampicin resistance result and 64 (53%) had true rifampicin resistance. A high pretest probability of rifampicin resistance did not decrease the odds of false rifampicin resistance (adjusted odds ratio [aOR] 6·0, 95% CI 1·0–35·0, for new tuberculosis patients vs patients who needed retreatment). Ten (16%) of the 64 patients with true rifampicin resistance did not have confirmed rifampicin resistance on repeat Xpert testing, of whom four had heteroresistance. Of 63 patients with a very low bacillary load on Xpert testing, 54 (86%) were falsely diagnosed with rifampicin-resistant tuberculosis. Having a very low bacillary load on Xpert testing was strongly associated with false rifampicin resistance at the initial Xpert assay (aOR 63·6, 95% CI 9·9–410·4). Interpretation: The Xpert testing algorithm should include an assessment of bacillary load and retesting in case rifampicin resistance is detected on a paucibacillary sputum sample. Only when rifampicin resistance has been confirmed on repeat testing should multidrug-resistant tuberculosis treatment be started. When rifampicin resistance has not been confirmed on repeat testing, we propose that patients should be given first-line anti-tuberculosis drugs and monitored closely during treatment, including by baseline culture, pDST, and further Xpert testing. Funding: The European & Developing Countries Clinical Trials Partnership 2 programme, and Belgian Directorate General for Development Cooperation.

Published
2020
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10. Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe [version 1; peer review: 2 approved, 1 approved with reservations]

Author

Martin Hunt, Phelim Bradley, Simon Grandjean Lapierre, Simon Heys, Mark Thomsit, Michael B. Hall, Kerri M. Malone, Penelope Wintringer, Timothy M. Walker, Daniela M. Cirillo, Iñaki Comas, Maha R. Farhat, Phillip Fowler, Jennifer Gardy, Nazir Ismail, Thomas A. Kohl, Vanessa Mathys, Matthias Merker, Stefan Niemann, Shaheed Vally Omar, Vitali Sintchenko, Grace Smith, Dick van Soolingen, Philip Supply, Sabira Tahseen, Mark Wilcox, Irena Arandjelovic, Tim E. A. Peto, Derrick W. Crook, and Zamin Iqbal

Subjects
Medicine, Science
Abstract

Two billion people are infected with Mycobacterium tuberculosis, leading to 10 million new cases of active tuberculosis and 1.5 million deaths annually. Universal access to drug susceptibility testing (DST) has become a World Health Organization priority. We previously developed a software tool, Mykrobe predictor, which provided offline species identification and drug resistance predictions for M. tuberculosis from whole genome sequencing (WGS) data. Performance was insufficient to support the use of WGS as an alternative to conventional phenotype-based DST, due to mutation catalogue limitations. Here we present a new tool, Mykrobe, which provides the same functionality based on a new software implementation. Improvements include i) an updated mutation catalogue giving greater sensitivity to detect pyrazinamide resistance, ii) support for user-defined resistance catalogues, iii) improved identification of non-tuberculous mycobacterial species, and iv) an updated statistical model for Oxford Nanopore Technologies sequencing data. Mykrobe is released under MIT license at https://github.com/mykrobe-tools/mykrobe. We incorporate mutation catalogues from the CRyPTIC consortium et al. (2018) and from Walker et al. (2015), and make improvements based on performance on an initial set of 3206 and an independent set of 5845 M. tuberculosis Illumina sequences. To give estimates of error rates, we use a prospectively collected dataset of 4362 M. tuberculosis isolates. Using culture based DST as the reference, we estimate Mykrobe to be 100%, 95%, 82%, 99% sensitive and 99%, 100%, 99%, 99% specific for rifampicin, isoniazid, pyrazinamide and ethambutol resistance prediction respectively. We benchmark against four other tools on 10207 (=5845+4362) samples, and also show that Mykrobe gives concordant results with nanopore data. We measure the ability of Mykrobe-based DST to guide personalized therapeutic regimen design in the context of complex drug susceptibility profiles, showing 94% concordance of implied regimen with that driven by phenotypic DST, higher than all other benchmarked tools.

Published
2019
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11. Compensatory evolution drives multidrug-resistant tuberculosis in Central Asia

Author

Matthias Merker, Maxime Barbier, Helen Cox, Jean-Philippe Rasigade, Silke Feuerriegel, Thomas Andreas Kohl, Roland Diel, Sonia Borrell, Sebastien Gagneux, Vladyslav Nikolayevskyy, Sönke Andres, Ulrich Nübel, Philip Supply, Thierry Wirth, and Stefan Niemann

Subjects
M. tuberculosis, drug resistance, MDR-TB, compensatory evolution, Medicine, Science, Biology (General), QH301-705.5
Abstract

Bacterial factors favoring the unprecedented multidrug-resistant tuberculosis (MDR-TB) epidemic in the former Soviet Union remain unclear. We utilized whole genome sequencing and Bayesian statistics to analyze the evolutionary history, temporal emergence of resistance and transmission networks of MDR Mycobacterium tuberculosis complex isolates from Karakalpakstan, Uzbekistan (2001–2006). One clade (termed Central Asian outbreak, CAO) dating back to 1974 (95% HPD 1969–1982) subsequently acquired resistance mediating mutations to eight anti-TB drugs. Introduction of standardized WHO-endorsed directly observed treatment, short-course in Karakalpakstan in 1998 likely selected for CAO-strains, comprising 75% of sampled MDR-TB isolates in 2005/2006. CAO-isolates were also identified in a published cohort from Russia (2008–2010). Similarly, the presence of mutations supposed to compensate bacterial fitness deficits was associated with transmission success and higher drug resistance rates. The genetic make-up of these MDR-strains threatens the success of both empirical and standardized MDR-TB therapies, including the newly WHO-endorsed short MDR-TB regimen in Uzbekistan.

Published
2018
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12. Set-up and validation of mycobacterial interspersed repetitive unit-variable number of tandem repeat (MIRU-VNTR) analysis of Mycobacterium tuberculosis using BioNumerics software.

Author

Mathias Klok Pedersen, Aase Bengaard Andersen, Dorte Bek Folkvardsen, Erik Michael Rasmussen, Erik Svensson, Troels Lillebaek, and Philip Supply

Subjects
Medicine, Science
Abstract

The objective was to describe and validate a new and alternative software procedure for 24-locus mycobacterial interspersed repetitive unit-variable number-tandem repeat (MIRU-VNTR) typing of Mycobacterium tuberculosis (Mtb) based on the multipurpose BioNumerics software. DNA from randomly selected isolates of Mtb from two European laboratories, including external control samples for MIRU-VNTR typing, were analysed. Samples were genotyped using the commercial 24-locus VNTR typing kit from GenoScreen. The PCR amplified fragments were separated by capillary electrophoresis. For the subsequent analyses, the currently used software GeneMapper was compared with BioNumerics. The endpoint was the level of concordance when comparing genotyping results obtained from BioNumerics with results obtained from GeneMapper and the ECDC proficiency study reference results. Also, the number of necessary manual standard size corrections and allele assignments in the two different software methods were compared. In total, 272 DNA samples, including the ECDC proficiency panel, were analysed. For all samples, there were 100% concordance of results. For a randomly selected set of 96 samples the numbers of manual corrections needed for size standards were 199 with GeneMapper versus zero for BioNumerics. The numbers of manual corrections for allele assignments were 122 with GeneMapper versus 16 with BioNumerics. In conclusion, we have validated the multipurpose software BioNumerics for standard 24-locus MIRU-VNTR typing and the software shows promising benefits in terms of simplification and minimization of hand-on time.

Published
2018
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13. Horizontal acquisition of a hypoxia-responsive molybdenum cofactor biosynthesis pathway contributed to Mycobacterium tuberculosis pathoadaptation.

Author

Florence Levillain, Yannick Poquet, Ludovic Mallet, Serge Mazères, Michael Marceau, Roland Brosch, Franz-Christoph Bange, Philip Supply, Axel Magalon, and Olivier Neyrolles

Subjects
Immunologic diseases. Allergy, RC581-607, Biology (General), QH301-705.5
Abstract

The unique ability of the tuberculosis (TB) bacillus, Mycobacterium tuberculosis, to persist for long periods of time in lung hypoxic lesions chiefly contributes to the global burden of latent TB. We and others previously reported that the M. tuberculosis ancestor underwent massive episodes of horizontal gene transfer (HGT), mostly from environmental species. Here, we sought to explore whether such ancient HGT played a part in M. tuberculosis evolution towards pathogenicity. We were interested by a HGT-acquired M. tuberculosis-specific gene set, namely moaA1-D1, which is involved in the biosynthesis of the molybdenum cofactor. Horizontal acquisition of this gene set was striking because homologues of these moa genes are present all across the Mycobacterium genus, including in M. tuberculosis. Here, we discovered that, unlike their paralogues, the moaA1-D1 genes are strongly induced under hypoxia. In vitro, a M. tuberculosis moaA1-D1-null mutant has an impaired ability to respire nitrate, to enter dormancy and to survive in oxygen-limiting conditions. Conversely, heterologous expression of moaA1-D1 in the phylogenetically closest non-TB mycobacterium, Mycobacterium kansasii, which lacks these genes, improves its capacity to respire nitrate and grants it with a marked ability to survive oxygen depletion. In vivo, the M. tuberculosis moaA1-D1-null mutant shows impaired survival in hypoxic granulomas in C3HeB/FeJ mice, but not in normoxic lesions in C57BL/6 animals. Collectively, our results identify a novel pathway required for M. tuberculosis resistance to host-imposed stress, namely hypoxia, and provide evidence that ancient HGT bolstered M. tuberculosis evolution from an environmental species towards a pervasive human-adapted pathogen.

Published
2017
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14. Predominance of Ancestral Lineages of Mycobacterium tuberculosis in India

Author

M. Cristina Gutierrez, Niyaz Ahmed, Eve Willery, Sujatha Narayanan, Seyed E. Hasnain, Devendra S. Chauhan, Vishwa M. Katoch, Véronique Vincent, Camille Locht, and Philip Supply

Subjects
tuberculosis, Mycobacterium tuberculosis, VNTR, spoligotyping, single nucleotide polymorphism, molecular epidemiology, Medicine, Infectious and parasitic diseases, RC109-216
Abstract

Although India has the highest prevalence of tuberculosis (TB) worldwide, the genetic diversity of Mycobacterium tuberculosis in India is largely unknown. A collection of 91 isolates originating from 12 different regions spread across the country were analyzed by genotyping using 21 loci with variable-number tandem repeats (VNTRs), by spoligotyping, by principal genetic grouping (PGG), and by deletion analysis of M. tuberculosis–specific deletion region 1. The isolates showed highly diverse VNTR genotypes. Nevertheless, highly congruent groupings identified by using the 4 independent sets of markers permitted a clear definition of 3 prevalent PGG1 lineages, which corresponded to the "ancestral" East African–Indian, the Delhi, and the Beijing/W genogroups. A few isolates from PGG2 lineages and a single representative of the presumably most recent PGG3 were identified. These observations suggest a predominance of ancestral M. tuberculosis genotypes in the Indian subcontinent, which supports the hypothesis that India is an ancient endemic focus of TB.

Published
2006
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15. Molecular Typing of Mycobacterium Tuberculosis Complex by 24-Locus Based MIRU-VNTR Typing in Conjunction with Spoligotyping to Assess Genetic Diversity of Strains Circulating in Morocco.

Author

Nada Bouklata, Philip Supply, Sanae Jaouhari, Reda Charof, Fouad Seghrouchni, Khalid Sadki, Youness El Achhab, Chakib Nejjari, Abdelkarim Filali-Maltouf, Ouafae Lahlou, and Rajae El Aouad

Subjects
Medicine, Science
Abstract

Standard 24-locus Mycobacterial Interspersed Repetitive Unit Variable Number Tandem Repeat (MIRU-VNTR) typing allows to get an improved resolution power for tracing TB transmission and predicting different strain (sub) lineages in a community.During 2010-2012, a total of 168 Mycobacterium tuberculosis Complex (MTBC) isolates were collected by cluster sampling from 10 different Moroccan cities, and centralized by the National Reference Laboratory of Tuberculosis over the study period. All isolates were genotyped using spoligotyping, and a subset of 75 was genotyped using 24-locus based MIRU-VNTR typing, followed by first line drug susceptibility testing. Corresponding strain lineages were predicted using MIRU-VNTRplus database.Spoligotyping resulted in 137 isolates in 18 clusters (2-50 isolates per cluster: clustering rate of 81.54%) corresponding to a SIT number in the SITVIT database, while 31(18.45%) patterns were unique of which 10 were labelled as "unknown" according to the same database. The most prevalent spoligotype family was LAM; (n = 81 or 48.24% of isolates, dominated by SIT42, n = 49), followed by Haarlem (23.80%), T superfamily (15.47%), >Beijing (2.97%), > U clade (2.38%) and S clade (1.19%). Subsequent 24-Locus MIRU-VNTR typing identified 64 unique types and 11 isolates in 5 clusters (2 to 3isolates per cluster), substantially reducing clusters defined by spoligotyping only. The single cluster of three isolates corresponded to two previously treated MDR-TB cases and one new MDR-TB case known to be contact a same index case and belonging to a same family, albeit residing in 3 different administrative regions. MIRU-VNTR loci 4052, 802, 2996, 2163b, 3690, 1955, 424, 2531, 2401 and 960 were highly discriminative in our setting (HGDI >0.6).24-locus MIRU-VNTR typing can substantially improve the resolution of large clusters initially defined by spoligotyping alone and predominating in Morocco, and could therefore be used to better study tuberculosis transmission in a population-based, multi-year sample context.

Published
2015
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16. Acquisition through horizontal gene transfer of plasmid pSMA198 by Streptococcus macedonicus ACA-DC 198 points towards the dairy origin of the species.

Author

Konstantinos Papadimitriou, Rania Anastasiou, Eleni Maistrou, Thomas Plakas, Nikos C Papandreou, Stavros J Hamodrakas, Stéphanie Ferreira, Philip Supply, Pierre Renault, Bruno Pot, and Effie Tsakalidou

Subjects
Medicine, Science
Abstract

BACKGROUND:Streptococcus macedonicus is an intriguing streptococcal species whose most frequent source of isolation is fermented foods similarly to Streptococcus thermophilus. However, S. macedonicus is closely related to commensal opportunistic pathogens of the Streptococcus bovis/Streptococcus equinus complex. METHODOLOGY/PRINCIPAL FINDINGS:We analyzed the pSMA198 plasmid isolated from the dairy strain Streptococcus macedonicus ACA-DC 198 in order to provide novel clues about the main ecological niche of this bacterium. pSMA198 belongs to the narrow host range pCI305/pWV02 family found primarily in lactococci and to the best of our knowledge it is the first such plasmid to be reported in streptococci. Comparative analysis of the pSMA198 sequence revealed a high degree of similarity with plasmids isolated from Lactococcus lactis strains deriving from milk or its products. Phylogenetic analysis of the pSMA198 Rep showed that the vast majority of closely related proteins derive from lactococcal dairy isolates. Additionally, cloning of the pSMA198 ori in L. lactis revealed a 100% stability of replication over 100 generations. Both pSMA198 and the chromosome of S. macedonicus exhibit a high percentage of potential pseudogenes, indicating that they have co-evolved under the same gene decay processes. We identified chromosomal regions in S. macedonicus that may have originated from pSMA198, also supporting a long co-existence of the two replicons. pSMA198 was also found in divergent biotypes of S. macedonicus and in strains isolated from dispersed geographic locations (e.g. Greece and Switzerland) showing that pSMA198's acquisition is not a recent event. CONCLUSIONS/SIGNIFICANCE:Here we propose that S. macedonicus acquired plasmid pSMA198 from L. lactis via an ancestral genetic exchange event that took place most probably in milk or dairy products. We provide important evidence that point towards the dairy origin of this species.

Published
2015
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17. Prospective genotyping of Mycobacterium tuberculosis from fresh clinical samples.

Author

Urška Bidovec-Stojkovič, Katja Seme, Manca Žolnir-Dovč, and Philip Supply

Subjects
Medicine, Science
Abstract

Shorter time-to-result is key for improving molecular-guided epidemiological investigation of tuberculosis (TB) cases. We performed a prospective study to evaluate the use of standardized MIRU-VNTR (mycobacterial interspersed repetitive-unit-variable-number tandem-repeat) typing of Mycobacterium tuberculosis directly on 79 fresh clinical samples from 26 TB patients consecutively enrolled over a 17-month period. Overall, complete 24-locus types were obtained for 18 out of the 26 (69.2%) patients and 14 of the 16 grade 3+ and grade 2+ samples (87.5%). The degree of completion of the genotypes obtained significantly correlated with smear microscopy grade both for 26 first samples (p = 0.0003) and for 53 follow-up samples (p = 0.002). For 20 of the 26 patients for whom complete or even incomplete M. tuberculosis isolate genotypes were obtained, typing applied to the clinical samples allowed the same unambiguous conclusions regarding case clustering or uniqueness as those that could have been drawn based on the corresponding cultured isolates. Standard 24 locus MIRU-VNTR typing of M. tuberculosis can be applied directly to fresh clinical samples, with typeability depending on the bacterial load in the sample.

Published
2014
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18. Admixed phylogenetic distribution of drug resistant Mycobacterium tuberculosis in Saudi Arabia.

Author

Bright Varghese, Philip Supply, Caroline Allix-Béguec, Mohammed Shoukri, Ruba Al-Omari, Mais Herbawi, and Sahal Al-Hajoj

Subjects
Medicine, Science
Abstract

BackgroundThe phylogeographical structure of Mycobacterium tuberculosis is generally bimodal in low tuberculosis (TB) incidence countries, where genetic lineages of the isolates generally differ with little strain clustering between autochthonous and foreign-born TB patients. However, less is known on this structure in Saudi Arabia-the most important hub of human migration as it hosts a total population of expatriates and pilgrims from all over the world which is equal to that of its citizens.MethodologyWe explored the mycobacterial phylogenetic structure and strain molecular clustering in Saudi Arabia by genotyping 322 drug-resistant clinical isolates collected over a 12-month period in a national drug surveillance survey, using 24 locus-based MIRU-VNTR typing and spoligotyping.Principal findingsIn contrast to the cosmopolitan population of the country, almost all the known phylogeographic lineages of M. tuberculosis complex (with noticeable exception of Mycobacterium africanum/West-African 1 and 2) were detected, with Delhi/CAS (21.1%), EAI (11.2%), Beijing (11.2%) and main branches of the Euro-American super-lineage such as Ghana (14.9%), Haarlem (10.6%) and Cameroon (7.8%) being represented. Statistically significant associations of strain lineages were observed with poly-drug resistance and multi drug resistance especially among previously treated cases (p value of ConclusionsSpecific distribution of M. tuberculosis phylogeographic lineages is not observed between the autochthonous and foreign-born populations. These observations might reflect both socially favored ongoing TB transmission between the two population groups, and historically deep-rooted, prolonged contacts and trade relations of the peninsula with other world regions. More vigorous surveillance and strict adherence to tuberculosis control policies are urgently needed in the country.

Published
2013
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19. Whole genome sequencing versus traditional genotyping for investigation of a Mycobacterium tuberculosis outbreak: a longitudinal molecular epidemiological study.

Author

Andreas Roetzer, Roland Diel, Thomas A Kohl, Christian Rückert, Ulrich Nübel, Jochen Blom, Thierry Wirth, Sebastian Jaenicke, Sieglinde Schuback, Sabine Rüsch-Gerdes, Philip Supply, Jörn Kalinowski, and Stefan Niemann

Subjects
Medicine
Abstract

BackgroundUnderstanding Mycobacterium tuberculosis (Mtb) transmission is essential to guide efficient tuberculosis control strategies. Traditional strain typing lacks sufficient discriminatory power to resolve large outbreaks. Here, we tested the potential of using next generation genome sequencing for identification of outbreak-related transmission chains.Methods and findingsDuring long-term (1997 to 2010) prospective population-based molecular epidemiological surveillance comprising a total of 2,301 patients, we identified a large outbreak caused by an Mtb strain of the Haarlem lineage. The main performance outcome measure of whole genome sequencing (WGS) analyses was the degree of correlation of the WGS analyses with contact tracing data and the spatio-temporal distribution of the outbreak cases. WGS analyses of the 86 isolates revealed 85 single nucleotide polymorphisms (SNPs), subdividing the outbreak into seven genome clusters (two to 24 isolates each), plus 36 unique SNP profiles. WGS results showed that the first outbreak isolates detected in 1997 were falsely clustered by classical genotyping. In 1998, one clone (termed "Hamburg clone") started expanding, apparently independently from differences in the social environment of early cases. Genome-based clustering patterns were in better accordance with contact tracing data and the geographical distribution of the cases than clustering patterns based on classical genotyping. A maximum of three SNPs were identified in eight confirmed human-to-human transmission chains, involving 31 patients. We estimated the Mtb genome evolutionary rate at 0.4 mutations per genome per year. This rate suggests that Mtb grows in its natural host with a doubling time of approximately 22 h (400 generations per year). Based on the genome variation discovered, emergence of the Hamburg clone was dated back to a period between 1993 and 1997, hence shortly before the discovery of the outbreak through epidemiological surveillance.ConclusionsOur findings suggest that WGS is superior to conventional genotyping for Mtb pathogen tracing and investigating micro-epidemics. WGS provides a measure of Mtb genome evolution over time in its natural host context.

Published
2013
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20. Tuberculosis transmission among immigrants and autochthonous populations of the eastern province of Saudi Arabia.

Author

Bright Varghese, Philip Supply, Mohammed Shoukri, Caroline Allix-Beguec, Ziad Memish, Naila Abuljadayel, Raafat Al-Hakeem, Fahad AlRabiah, and Sahal Al-Hajoj

Subjects
Medicine, Science
Abstract

BACKGROUND:Eastern province of Saudi Arabia is an industrial zone with large immigrant population and high level of tuberculosis case notification among immigrants. The impact of immigration and current trends of tuberculosis transmission among immigrants and autochthonous population in the region had not been investigated so far using molecular tools. METHODOLOGY:During 2009- 2011, a total of 524 Mycobacterium tuberculosis isolates were collected from the central tuberculosis reference laboratory, representing an estimated 79.2% of the culture-positive tuberculosis cases over the study period in the province. These isolates were genotyped by using 24 locus-based MIRU-VNTR typing and spoligotyping followed by first line drug susceptibility testing. The molecular clustering profiles and phylogenetic diversity of isolates were determined and compared to the geographical origins of the patients. PRINCIPLE FINDINGS:Genotyping showed an overall predominance of Delhi/CAS (29.4%), EAI (23.8%) and Ghana (13.3%) lineages, with slightly higher proportions of Delhi/CAS among autochthonous population (33.3 %) and EAI (30.9%) among immigrants. Rate of any drug resistance was 20.2% with 2.5% of multi-drug resistance. Strain cluster analysis indicated 42 clusters comprising 210 isolates, resulting in a calculated recent transmission index of 32.1%. Overall shared cluster ratio was 78.6% while 75.8% were shared between autochthonous population and immigrant population with a predominance of immigrants from South east Asia (40.7%). In contrast, cross national transmission within the immigrant population was limited (24.2%). Younger age (15-30- p value-0.043, 16-45, p value 0.030), Saudi nationality (p value-0.004) and South East Asian origin (p value-0.011) were identified as significant predisposing factors for molecular strain clustering. CONCLUSIONS:The high proportion of molecular clusters shared among the autochthonous and immigrant populations suggests a high permeability of tuberculosis transmission between both populations in the province. These results prompt for the need to strengthen the current tuberculosis control strategies and surveillance programs.

Published
2013
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21. From multidrug- to extensively drug-resistant tuberculosis: upward trends as seen from a 15-year nationwide study.

Author

Karolien Stoffels, Caroline Allix-Béguec, Guido Groenen, Maryse Wanlin, Dirk Berkvens, Vanessa Mathys, Philip Supply, and Maryse Fauville-Dufaux

Subjects
Medicine, Science
Abstract

BackgroundEmergence of extensively drug-resistant tuberculosis (XDR-TB) represents an enormous challenge to Public Health globally.MethodsProgression towards XDR-TB was investigated in Belgium, a country with a typically low TB incidence, by analyzing the magnitude, characteristics, and treatment success of multidrug-resistant tuberculosis (MDR-TB) through a population-based study from 1994 to 2008.ResultsAmong the 174 MDR-TB patients, 81% were foreign-born, 48% of these being asylum seekers. Although the number of MDR-TB patients remained stable through the study period at around 15 new cases annually, frequencies of resistance of the patients' first MDR-TB isolate to second-line drugs increased, as well as the total number of antibiotics it was resistant to (pConclusionsIncreasing severity in drug resistance patterns leading to more XDR- and "panresistant" TB cases in a country with a low TB incidence like Belgium represents a strong alert on worsening situations in other world regions and requires intense public health measures.

Published
2013
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22. The forest behind the tree: phylogenetic exploration of a dominant Mycobacterium tuberculosis strain lineage from a high tuberculosis burden country.

Author

Maranibia Cardoso Oelemann, Harrison M Gomes, Eve Willery, Lia Possuelo, Karla Valéria Batista Lima, Caroline Allix-Béguec, Camille Locht, Yves-Olivier L Goguet de la Salmonière, Maria Cristina Gutierrez, Philip Suffys, and Philip Supply

Subjects
Medicine, Science
Abstract

BackgroundGenotyping of Mycobacterium tuberculosis isolates is a powerful tool for epidemiological control of tuberculosis (TB) and phylogenetic exploration of the pathogen. Standardized PCR-based typing, based on 15 to 24 mycobacterial interspersed repetitive unit-variable number of tandem repeat (MIRU-VNTR) loci combined with spoligotyping, has been shown to have adequate resolution power for tracing TB transmission and to be useful for predicting diverse strain lineages in European settings. Its informative value needs to be tested in high TB-burden countries, where the use of genotyping is often complicated by dominance of geographically specific, genetically homogeneous strain lineages.Methodology/principal findingsWe tested this genotyping system for molecular epidemiological analysis of 369 M. tuberculosis isolates from 3 regions of Brazil, a high TB-burden country. Deligotyping, targeting 43 large sequence polymorphisms (LSPs), and the MIRU-VNTRplus identification database were used to assess phylogenetic predictions. High congruence between the different typing results consistently revealed the countrywide supremacy of the Latin-American-Mediterranean (LAM) lineage, comprised of three main branches. In addition to an already known RDRio branch, at least one other branch characterized by a phylogenetically informative LAM3 spoligo-signature seems to be globally distributed beyond Brazil. Nevertheless, by distinguishing 321 genotypes in this strain population, combined MIRU-VNTR typing and spoligotyping demonstrated the presence of multiple distinct clones. The use of 15 to 24 loci discriminated 21 to 25% more strains within the LAM lineage, compared to a restricted lineage-specific locus set suggested to be used after SNP analysis. Noteworthy, 23 of the 28 molecular clusters identified were exclusively composed of patient isolates from a same region, consistent with expected patterns of mostly local TB transmission.Conclusions/significanceStandard MIRU-VNTR typing combined with spoligotyping can reveal epidemiologically meaningful clonal diversity behind a dominant M. tuberculosis strain lineage in a high TB-burden country and is useful to explore international phylogenetical ramifications.

Published
2011
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23. Origin, spread and demography of the Mycobacterium tuberculosis complex.

Author

Thierry Wirth, Falk Hildebrand, Caroline Allix-Béguec, Florian Wölbeling, Tanja Kubica, Kristin Kremer, Dick van Soolingen, Sabine Rüsch-Gerdes, Camille Locht, Sylvain Brisse, Axel Meyer, Philip Supply, and Stefan Niemann

Subjects
Immunologic diseases. Allergy, RC581-607, Biology (General), QH301-705.5
Abstract

The evolutionary timing and spread of the Mycobacterium tuberculosis complex (MTBC), one of the most successful groups of bacterial pathogens, remains largely unknown. Here, using mycobacterial tandem repeat sequences as genetic markers, we show that the MTBC consists of two independent clades, one composed exclusively of M. tuberculosis lineages from humans and the other composed of both animal and human isolates. The latter also likely derived from a human pathogenic lineage, supporting the hypothesis of an original human host. Using Bayesian statistics and experimental data on the variability of the mycobacterial markers in infected patients, we estimated the age of the MTBC at 40,000 years, coinciding with the expansion of "modern" human populations out of Africa. Furthermore, coalescence analysis revealed a strong and recent demographic expansion in almost all M. tuberculosis lineages, which coincides with the human population explosion over the last two centuries. These findings thus unveil the dynamic dimension of the association between human host and pathogen populations.

Published
2008
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25. Ancient origin and gene mosaicism of the progenitor of Mycobacterium tuberculosis.

Author

M Cristina Gutierrez, Sylvain Brisse, Roland Brosch, Michel Fabre, Bahia Omaïs, Magali Marmiesse, Philip Supply, and Veronique Vincent

Subjects
Immunologic diseases. Allergy, RC581-607, Biology (General), QH301-705.5
Abstract

The highly successful human pathogen Mycobacterium tuberculosis has an extremely low level of genetic variation, which suggests that the entire population resulted from clonal expansion following an evolutionary bottleneck around 35,000 y ago. Here, we show that this population constitutes just the visible tip of a much broader progenitor species, whose extant representatives are human isolates of tubercle bacilli from East Africa. In these isolates, we detected incongruence among gene phylogenies as well as mosaic gene sequences, whose individual elements are retrieved in classical M. tuberculosis. Therefore, despite its apparent homogeneity, the M. tuberculosis genome appears to be a composite assembly resulting from horizontal gene transfer events predating clonal expansion. The amount of synonymous nucleotide variation in housekeeping genes suggests that tubercle bacilli were contemporaneous with early hominids in East Africa, and have thus been coevolving with their human host much longer than previously thought. These results open novel perspectives for unraveling the molecular bases of M. tuberculosis evolutionary success.

Published
2005
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26. Investigating drug resistance of Mycobacterium leprae in the Comoros: an observational deep-sequencing study

Author

Sofie Marijke Braet, Agathe Jouet, Alexandra Aubry, Magalie Van Dyck-Lippens, Esteban Lenoir, Younoussa Assoumani, Abdallah Baco, Aboubacar Mzembaba, Emmanuelle Cambau, Sidra Ezidio Gonçalves Vasconcellos, Leen Rigouts, Philip Noel Suffys, Epco Hasker, Philip Supply, Bouke Catherine de Jong, University of Antwerp (UA), Institute of Tropical Medicine [Antwerp] (ITM), Genoscreen [Lille], Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Centre d'Immunologie et des Maladies Infectieuses (CIMI), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Centre National de Référence des Mycobactéries et de la Résistance aux Antituberculeux [CHU Pitié-Salpêtrière] (CNR-MyRMA), CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Damien Foundation, Infection, Anti-microbiens, Modélisation, Evolution (IAME (UMR_S_1137 / U1137)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité)-Université Sorbonne Paris Nord, AP-HP - Hôpital Bichat - Claude Bernard [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Instituto Oswaldo Cruz / Oswaldo Cruz Institute [Rio de Janeiro] (IOC), Fundação Oswaldo Cruz (FIOCRUZ), Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204 (CIIL), Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Centre National de la Recherche Scientifique (CNRS), CHU Lille, Supply, Philip, Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), and Fundação Oswaldo Cruz / Oswaldo Cruz Foundation (FIOCRUZ)

Subjects
Microbiology (medical), [SDV.GEN]Life Sciences [q-bio]/Genetics, Leprostatic Agents, [SDV.GEN] Life Sciences [q-bio]/Genetics, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Microbiology, Comoros, Mycobacterium leprae, Infectious Diseases, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Leprosy, Virology, Drug Resistance, Bacterial, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Humans, Drug Therapy, Combination, Human medicine, Rifampin, [SDV.MP.BAC] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Dapsone, Biology
Abstract

Despite strong leprosy control measures, including effective treatment, leprosy persists in the Comoros. As of May, 2022, no resistance to anti-leprosy drugs had been reported, but there are no nationally representative data. Post-exposure prophylaxis (PEP) with rifampicin is offered to contacts of patients with leprosy. We aimed to conduct a countrywide drug resistance survey and investigate whether PEP led to the emergence of drug resistance in patients with leprosy.In this observational, deep-sequencing analysis we assessed Mycobacterium leprae genomes from skin biopsies of patients in Anjouan and Mohéli, Comoros, collected as part of the ComLep (NCT03526718) and PEOPLE (NCT03662022) studies. Skin biopsies that had sufficient M leprae DNA (2000 bacilli in 2 μl of DNA extract) were assessed for the presence of seven drug resistance-associated genes (ie, rpoB, ctpC, ctpI, folP1, gyrA, gyrB, and nth) using Deeplex Myc-Lep (targeted next generation deep sequencing), with a limit of detection of 10% for minority M leprae bacterial populations bearing a polymorphism in these genes. All newly registered patients with leprosy for whom written informed consent was obtained were eligible for inclusion in the survey. Patients younger than 2 years or with a single lesion on the face did not have biopsies taken. The primary outcome of our study was the proportion of patients with leprosy (ie, new cases, patients with relapses or reinfections, patients who received single (double) dose rifampicin-PEP, or patients who lived in villages where PEP was distributed) who were infected with M leprae with a drug-resistant mutation for rifampicin, fluoroquinolone, or dapsone in the Comoros.Between July 1, 2017, and Dec 31, 2020, 1199 patients with leprosy were identified on the basis of clinical criteria, of whom 1030 provided a skin biopsy. Of these 1030 patients, 755 (73·3%) tested positive for the M leprae-specific repetitive element-quantitative PCR (qPCR) assay. Of these 755 patients, 260 (34·4%) were eligible to be analysed using Deeplex Myc-Lep. 251 (96·5%) were newly diagnosed with leprosy, whereas nine (3·4%) patients had previously received multidrug therapy. 45 (17·3%) patients resided in villages where PEP had been administered in 2015 or 2019, two (4·4%) of whom received PEP. All seven drug resistance-associated targets were successfully sequenced in 216 samples, 39 samples had incomplete results, and five had no results. No mutations were detected in any of the seven drug resistance-related genes for any patient with successfully sequenced results.This drug resistance survey provides evidence to show that M leprae is fully susceptible to rifampicin, fluoroquinolones, and dapsone in the Comoros. Our results also show, for the first time, the applicability of targeted sequencing directly on skin biopsies from patients with either paucibacillary or multibacillary leprosy. These data suggest that PEP had not selected rifampicin-resistant strains, although further support for this finding should be confirmed with a larger sample size.Effect:Hope, The Mission To End Leprosy, the Fonds Wetenschappelijk Onderzoek, the EU.

Published
2022
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28. Origin and Global Expansion of

Author

Yassir A, Shuaib, Christian, Utpatel, Thomas A, Kohl, Ivan, Barilar, Margo, Diricks, Nadia, Ashraf, Lothar H, Wieler, Glennah, Kerubo, Eyob A, Mesfin, Awa Ba, Diallo, Sahal, Al-Hajoj, Perpetua, Ndung'u, Margaret M, Fitzgibbon, Farzam, Vaziri, Vitali, Sintchenko, Elena, Martinez, Sofia O, Viegas, Yang, Zhou, Aya, Azmy, Khaled, Al-Amry, Sylvain, Godreuil, Mandira, Varma-Basil, Anshika, Narang, Solomon, Ali, Patrick, Beckert, Viola, Dreyer, Mwila, Kabwe, Matthew, Bates, Michael, Hoelscher, Andrea, Rachow, Andrea, Gori, Emmanuel M, Tekwu, Larissa K, Sidze, Assam A, Jean-Paul, Veronique P, Beng, Francine, Ntoumi, Matthias, Frank, Aissatou Gaye, Diallo, Souleymane, Mboup, Belay, Tessema, Dereje, Beyene, Sadiq N, Khan, Roland, Diel, Philip, Supply, Florian P, Maurer, Harald, Hoffmann, Stefan, Niemann, and Matthias, Merker

Subjects
Genotype, Microbial Sensitivity Tests, Minisatellite Repeats, Mycobacterium tuberculosis, Phylogeny
Published
2022

29. Balancing access to BPaLM regimens and risk of resistance

Author

Annelies Van Rie, Timothy Walker, Bouke de Jong, Praharshinie Rupasinghe, Emmanuel Rivière, Véronique Dartois, Lindsay Sonnenkalb, Diana Machado, Sébastien Gagneux, Philip Supply, Viola Dreyer, Stefan Niemann, Galo Goig, Conor Meehan, Elisa Tagliani, Daniela Maria Cirillo, Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204 (CIIL), Institut Pasteur de Lille, and Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Infectious Diseases, [SDV]Life Sciences [q-bio], Human medicine
Abstract

International audience

Published
2022
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30. Epidemiological cutoff values for a 96-well broth microdilution plate for high-throughput research antibiotic susceptibility testing of M. tuberculosis

Author

Zamin Iqbal, Timothy Walker, Philip Supply, Matthias Merker, Pénélope Wintringer, Kerri M Malone, Derrick Crook, Samaneh Kouchaki, Philip Fowler, and Gillian Rodger

Subjects
Susceptibility testing, education.field_of_study, Veterinary medicine, Tuberculosis, medicine.drug_class, Population, Broth microdilution, Antibiotics, Biology, medicine.disease, chemistry.chemical_compound, chemistry, medicine, Cutoff, Delamanid, Bedaquiline, education, medicine.drug
Abstract

Drug susceptibility testing of M. tuberculosis is rooted in a binary susceptible/resistant paradigm.Whilst there are considerable advantages in measuring the minimum inhibitory concentrations (MICs) of a panel of drugs for an isolate it is n ecessary to measure the epidemiological cutoff values (ECOFF/ECVs) to permit comparison with qualitative data. Here we present ECOFF/ECVs for 13 anti-TB compounds, including bedaquiline and delamanid, derived from 20,637 clinical isolates collected by 14 laboratories based in 11 countries on five continents. Each isolate was incubated for 14 days on a dry 96-well broth microdilution plate and then read. Resistance to most of the drugs due to prior exposure is expected and the MIC distributions for many of the compounds are complex and therefore a phenotypically wild-type population could not be defined. Since a majority of samples also underwent genetic sequencing, we defined a genotypically wild-type population and measured the MIC of the 99th percentile by direct measurement and via fitting a Gaussian using interval regression.The proposed ECOFF/ECV values were then validated by comparing to the MIC distributions of high-confidence genetic variants that confer resistance and to qualitative drug susceptibility tests obtained via Mycobacterial Growth Indicator Tube and the Microscopic-Observation Drug-Susceptibility assay.These ECOFF/ECV values will inform and encourage the more widespread adoption of broth microdilution – this is a cheap culture-based method that tests the susceptibility of 12-14 antibiotics on a single 96-well plate and so could help personalise the treatment of tuberculosis.

Published
2021
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31. Rapid genomic first- and second-line drug resistance prediction from clinical Mycobacterium tuberculosis specimens using Deeplex®-MycTB

Author

Thomas Kohl, Osman S. Conteh, Silke Feuerriegel, Agathe Jouet, Jan Heyckendorf, Rashidatu Fouad Kamara, Stefan Niemann, Nelly Badalato, Florian P. Maurer, Christian Utpatel, Philip Supply, Sönke Andres, Lynda Foray, Forschungszentrum Borstel - Research Center Borstel, German Centre for Infection Research - partner site Hamburg-Lübeck-Borstel-Riems (DZIF), Universitaetsklinikum Hamburg-Eppendorf = University Medical Center Hamburg-Eppendorf [Hamburg] (UKE), Universität zu Lübeck [Lübeck], Genoscreen [Lille], Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Ministry of Health [Sierra Leone], Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204 (CIIL), Centre National de la Recherche Scientifique (CNRS)-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Université de Lille-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur de Lille, his work was supported by the European Commission (grant: FP7- 278864), Deutsches Zentrum für Infektionsforschung, Joachim Herz Stiftung, Leibniz Science Campus Evolutionary Medicine of the LUNG and Deutsche Forschungsgemeinschaft (grant: Precision Medicine in Chronic Inflammation EXC 216)., European Project: 278864,EC:FP7:HEALTH,FP7-HEALTH-2011-two-stage,PATHONGEN-TRACE(2012), Universität zu Lübeck = University of Lübeck [Lübeck], and Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Pulmonary and Respiratory Medicine, Tuberculosis, biology, business.industry, Internet privacy, Conflict of interest, MEDLINE, Evolutionary medicine, Resistance (psychoanalysis), Precision medicine, biology.organism_classification, medicine.disease, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, [SDV.MHEP.PSR]Life Sciences [q-bio]/Human health and pathology/Pulmonology and respiratory tract, 3. Good health, Mycobacterium tuberculosis, 03 medical and health sciences, 0302 clinical medicine, 030228 respiratory system, Nothing, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Medicine, 030212 general & internal medicine, business, ComputingMilieux_MISCELLANEOUS
Abstract

The emergence of multidrug-resistant (MDR) and extensively-drug-resistant (XDR-TB) Mycobacterium tuberculosis complex (Mtbc) isolates challenges tuberculosis (TB) control worldwide [1] and requires the rapid determination of extensive resistance profiles [2], enabling prompt initiation of effective treatment regimens. Phenotypic drug susceptibility testing (pDST) takes up to six weeks [3], and is unreliable and/or not standardised for several drugs according to WHO guidelines [4]. Molecular DST (mDST) assays, like Xpert MTB/RIF (Cepheid) or MTBDR plus / sl line probe assays (LPAs, Hain Lifesciences) can be performed directly from clinical specimens, but only target a limited number of resistance variants [5]. Footnotes This manuscript has recently been accepted for publication in the European Respiratory Journal . It is published here in its accepted form prior to copyediting and typesetting by our production team. After these production processes are complete and the authors have approved the resulting proofs, the article will move to the latest issue of the ERJ online. Please open or download the PDF to view this article. Conflict of interest: Dr. Andres has nothing to disclose. Conflict of interest: Dr. Badalato reports personal fees from GenoScreen, during the conduct of the study; personal fees from GenoScreen, outside the submitted work. Conflict of interest: Dr. Conteh has nothing to disclose. Conflict of interest: Dr. Feuerriegel has nothing to disclose. Conflict of interest: Dr. Foray has nothing to disclose. Conflict of interest: Dr. Fouad Kamara has nothing to disclose. Conflict of interest: Dr. Heyckendorf has nothing to disclose. Conflict of interest: Dr. Jouet reports personal fees from GenoScreen, during the conduct of the study. Conflict of interest: Dr. Kohl has nothing to disclose. Conflict of interest: Dr. Maurer has nothing to disclose. Conflict of interest: Dr. Niemann reports grants from German Center for Infection Research, grants from Excellenz Cluster Precision Medicine in Chronic Inflammation EXC 2167, grants from Leibniz Science Campus Evolutionary Medicine of the LUNG (EvoLUNG), during the conduct of the study. Conflict of interest: Dr. Supply reports personal fees from Genoscreen, during the conduct of the study. Conflict of interest: Dr. Utpatel has nothing to disclose.

Published
2021
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32. Case Report: Dynamics of Acquired Fluoroquinolone Resistance under Standardized Short-Course Treatment of Multidrug-Resistant Tuberculosis

Author

Armand Van Deun, Bertin Ushizimpumu, Wim Mulders, Patrick Migambi, Leen Rigouts, Philip Supply, Jean Claude Semuto Ngabonziza, Bouke C. de Jong, Théogène Dusabe, Tom Decroo, Esdras Belamo Niyigena, Yves Mucyo Habimana, Dissou Affolabi, Rwanda Biomedical Center (RBC), Institute of Tropical Medicine [Antwerp] (ITM), Universiteit Antwerpen [Antwerpen], Kabutare Hospital [Huye, Rwanda], Research Foundation - Flanders [Brussel] (FWO), Laboratoire de Référence des Mycobactéries [Cotonou, Benin], Hôpital Centre LAZARET [Cotonou, Bénin], Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204 (CIIL), Centre National de la Recherche Scientifique (CNRS)-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Université de Lille-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), This publication is based on findings produced inthe context of the DIAMA study, which is part of the EDCTP2 program supported by the European Union (Grant number DRIA2014-326—DIAMA) and the Belgian Directorate General for Development Cooperation (PhD fellowship to JCSN). P. S. reports personal fees from GenoScreen during the conduct of the study., Universiteit Antwerpen = University of Antwerpen [Antwerpen], Institut Pasteur de Lille, and Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Centre National de la Recherche Scientifique (CNRS)

Subjects
medicine.medical_specialty, Tuberculosis, [SDV]Life Sciences [q-bio], Moxifloxacin, 030231 tropical medicine, Antitubercular Agents, Microbial Sensitivity Tests, Drug resistance, Clofazimine, Gatifloxacin, 03 medical and health sciences, 0302 clinical medicine, Kanamycin, Drug Resistance, Multiple, Bacterial, Virology, Internal medicine, Tuberculosis, Multidrug-Resistant, Humans, Medicine, business.industry, Rwanda, High-Throughput Nucleotide Sequencing, Articles, Mycobacterium tuberculosis, Sequence Analysis, DNA, Middle Aged, medicine.disease, Fluoroquinolone resistance, 3. Good health, Multiple drug resistance, Infectious Diseases, Genes, Bacterial, Female, Parasitology, Human medicine, business, Fluoroquinolones, medicine.drug
Abstract

International audience; We report a case of acquired fluoroquinolone (FQ) resistance under short-course multidrug-resistant tuberculosis (MDR-TB) treatment. The patient was managed at Kabutare hospital, one of the two specialized MDR-TB clinics in Rwanda. A low dose of moxifloxacin was used in the first three critical months. Acquired resistance was identified at the ninth month of treatment, 3 months after stopping kanamycin in a strain initially susceptible only to FQs, kanamycin, and clofazimine. Fluoroquinolone resistance was detected in the same month by deep sequencing as routinely used second-line line probe assay and phenotypic drug susceptibility testing. High-dose FQ, preferably gatifloxacin, should be used to maximize effectiveness.

Published
2020
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33. Deep amplicon sequencing for culture-free prediction of susceptibility or resistance to 13 anti-tuberculous drugs

Author

Cyril Gaudin, Stefan Niemann, Alice Ferré, Stéphanie Duthoy, Vanessa Mathys, Yannick Laurent, Emmanuel André, Elisa Tagliani, Bouke C. de Jong, Philip Supply, Andrea M. Cabibbe, Silke Feuerriegel, Caroline Allix-Béguec, Nelly Badalato, Sandy Contreras, Michel K. Kaswa, Leen Rigouts, Agathe Jouet, Daniela Maria Cirillo, Maren Diels, Institute of Tropical Medicine [Antwerp] (ITM), Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Universiteit Antwerpen [Antwerpen], Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204 (CIIL), Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Centre National de la Recherche Scientifique (CNRS), Genoscreen [Lille], Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Forschungszentrum Borstel - Research Center Borstel, German Centre for Infection Research - partner site Hamburg-Lübeck-Borstel-Riems (DZIF), National Tuberculosis Program [Kinshasa], IRCCS Ospedale San Raffaele [Milan, Italy], Maladies bactériennes = Bacterial diseases [Bruxelles], Sciensano [Bruxelles], Centre National de la Recherche Scientifique (CNRS)-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Université de Lille-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur de Lille, Parts of this work have been supported by the European Union PathoNGen-Trace project (FP7-278864) and by the World Health Organization (for the TB drug resistance survey conducted in the Democratic Republic of the Congo). B.C. de Jong and L. Rigouts were supported by European Research Council starting grant 'INTERRUPTB' (grant agreement 311725)., European Project: 278864,EC:FP7:HEALTH,FP7-HEALTH-2011-two-stage,PATHONGEN-TRACE(2012), European Project: 311725,EC:FP7:ERC,ERC-2012-StG_20111109,INTERRUPTB(2013), Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204 [CIIL], Universiteit Antwerpen = University of Antwerpen [Antwerpen], Noel, Anne-Laure, Next Generation Genome Based High Resolution Tracing of Pathogens - PATHONGEN-TRACE - - EC:FP7:HEALTH2012-01-01 - 2016-06-30 - 278864 - VALID, and Estimating the effective reproductive rate of M. tuberculosis from changes in molecular clustering rates, to measure the impact of public health interventions on TB transmission - INTERRUPTB - - EC:FP7:ERC2013-01-01 - 2017-12-31 - 311725 - VALID

Subjects
0301 basic medicine, Pulmonary and Respiratory Medicine, 030106 microbiology, Respiratory System, Antitubercular Agents, Drug resistance, Microbial Sensitivity Tests, [SDV.MHEP.PSR]Life Sciences [q-bio]/Human health and pathology/Pulmonology and respiratory tract, Deep sequencing, Mycobacterium, 03 medical and health sciences, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Tuberculosis, Multidrug-Resistant, medicine, Humans, Tuberculosis, Deeplex Myc-TB may enable fast, Ethambutol, Genetics, Whole genome sequencing, Science & Technology, biology, business.industry, High-Throughput Nucleotide Sequencing, Original Articles, Mycobacterium tuberculosis, Pyrazinamide, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 3. Good health, 030104 developmental biology, Mycobacterium tuberculosis complex, Pharmaceutical Preparations, Pulmonary Infections and Tuberculosis, Mutation, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, [SDV.MHEP.PSR] Life Sciences [q-bio]/Human health and pathology/Pulmonology and respiratory tract, Ethionamide, tailored tuberculosis treatment, Human medicine, [SDV.MP.BAC] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, business, Life Sciences & Biomedicine, Rifampicin, medicine.drug
Abstract

Conventional molecular tests for detecting Mycobacterium tuberculosis complex (MTBC) drug resistance on clinical samples cover a limited set of mutations. Whole-genome sequencing (WGS) typically requires culture. Here, we evaluated the Deeplex Myc-TB targeted deep-sequencing assay for prediction of resistance to 13 anti-tuberculous drugs/drug classes, directly applicable on sputum. With MTBC DNA tests, the limit of detection was 100–1000 genome copies for fixed resistance mutations. Deeplex Myc-TB captured in silico 97.1–99.3% of resistance phenotypes correctly predicted by WGS from 3651 MTBC genomes. On 429 isolates, the assay predicted 92.2% of 2369 first- and second-line phenotypes, with a sensitivity of 95.3% and a specificity of 97.4%. 56 out of 69 (81.2%) residual discrepancies with phenotypic results involved pyrazinamide, ethambutol and ethionamide, and low-level rifampicin or isoniazid resistance mutations, all notoriously prone to phenotypic testing variability. Only two out of 91 (2.2%) resistance phenotypes undetected by Deeplex Myc-TB had known resistance-associated mutations by WGS analysis outside Deeplex Myc-TB targets. Phenotype predictions from Deeplex Myc-TB analysis directly on 109 sputa from a Djibouti survey matched those of MTBSeq/PhyResSE/Mykrobe, fed with WGS data from subsequent cultures, with a sensitivity of 93.5/98.5/93.1% and a specificity of 98.5/97.2/95.3%, respectively. Most residual discordances involved gene deletions/indels and 3–12% heteroresistant calls undetected by WGS analysis or natural pyrazinamide resistance of globally rare “Mycobacterium canettii” strains then unreported by Deeplex Myc-TB. On 1494 arduous sputa from a Democratic Republic of the Congo survey, 14 902 out of 19 422 (76.7%) possible susceptible or resistance phenotypes could be predicted culture-free. Deeplex Myc-TB may enable fast, tailored tuberculosis treatment., The novel Deeplex Myc-TB molecular assay shows a high degree of accuracy for extensive prediction of susceptibility and resistance to 13 anti-tuberculous drugs, directly achievable without culture, which may enable fast, tailored tuberculosis treatment https://bit.ly/3bAvcAt

Published
2020
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34. Rapid genomic first- and second-line drug resistance prediction from clinical

Author

Silke, Feuerriegel, Thomas A, Kohl, Christian, Utpatel, Sönke, Andres, Florian P, Maurer, Jan, Heyckendorf, Agathe, Jouet, Nelly, Badalato, Lynda, Foray, Rashidatu, Fouad Kamara, Osman S, Conteh, Philip, Supply, and Stefan, Niemann

Subjects
Drug Resistance, Multiple, Bacterial, Drug Resistance, Bacterial, Tuberculosis, Multidrug-Resistant, Antitubercular Agents, Drug Resistance, Humans, Genomics, Microbial Sensitivity Tests, Mycobacterium tuberculosis
Published
2020

35. Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe

Author

Jennifer L. Gardy, Phillip Fowler, Simon Heys, Kerri M. Malone, Vanessa Mathys, Phelim Bradley, Penelope Wintringer, Timothy M Walker, Simon Grandjean Lapierre, Martin Hunt, Iñaki Comas, Dick van Soolingen, Vitali Sintchenko, Thomas Kohl, Sabira Tahseen, Zamin Iqbal, Grace Smith, Mark Thomsit, Shaheed V. Omar, Derrick W. Crook, Tim E. A. Peto, Philip Supply, Daniela Maria Cirillo, Maha R. Farhat, Stefan Niemann, Matthias Merker, Nazir Ahmed Ismail, Mark H. Wilcox, Michael B Hall, Irena Arandjelovic, European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, University of Oxford [Oxford], Centre Hospitalier de l'Université de Montréal (CHUM), Université de Montréal (UdeM), Oxford University Clinical Research Unit [Ho Chi Minh City] (OUCRU), IRCCS Ospedale San Raffaele [Milan, Italy], Instituto de biomedicina [Valencia] (IBV), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana [Espagne] (FISABIO), CIBER de Epidemiología y Salud Pública (CIBERESP), Harvard Medical School [Boston] (HMS), British Columbia Centre for Disease Control [Vancouver] (BCCDC), Bill & Melinda Gates Foundation [Seattle], National Institute for Communicable Diseases [Johannesburg] (NICD), Forschungszentrum Borstel - Research Center Borstel, Maladies bactériennes = Bacterial diseases [Bruxelles], Sciensano [Bruxelles], Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), German Center for Infection Research - Partner Site Hamburg-Lübeck-Borstel-Riems, German Centre for Infection Research (DZIF), The University of Sydney, Public Health England - Midlands and east of England regional office [Birmimgham], Public Health England [London], National Institute for Public Health and the Environment [Bilthoven] (RIVM), Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204 (CIIL), Centre National de la Recherche Scientifique (CNRS)-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Université de Lille-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur de Lille, National TB control Program [Islamabad, Pakistan], Leeds Teaching Hospitals NHS Trust, University of Leeds, University of Belgrade [Belgrade], ZI was funded by a Wellcome Trust/Royal Society Sir Henry Dale Fellowship, grant number 102541. MH was supported by Wellcome Trust/Newton Fund-MRC Collaborative Award [200205], and Bill & Melinda Gates Foundation Trust [OPP1133541]. TMW is a Wellcome Trust Clinical Career Development Fellow, grant number 214560., Royal Society (UK), Newton Fund, Bill & Melinda Gates Foundation, University of Oxford, Institut Pasteur de Lille, and Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0301 basic medicine, Nanopore, Tuberculosis, antibiotic treatment Reviewer Status, [SDV]Life Sciences [q-bio], 030106 microbiology, Medicine (miscellaneous), diagnostic, Context (language use), Computational biology, Drug resistance, Biology, Antimicrobial resistance, General Biochemistry, Genetics and Molecular Biology, Mycobacterium tuberculosis, 03 medical and health sciences, medicine, Diagnostic, nanopore, Ethambutol, whole genome sequencing, Software Tool Article, Articles, Pyrazinamide, biology.organism_classification, medicine.disease, Antibiotic treatment, 3. Good health, 030104 developmental biology, tuberculosis, Whole genome sequencing, Nanopore sequencing, Rifampicin, medicine.drug
Abstract

32 páginas, 7figuras, 9 tablas. This project contains European Nucleotide Archive accession numbers for Illumina sequence data and associated metatdata, Two billion people are infected with Mycobacterium tuberculosis, leading to 10 million new cases of active tuberculosis and 1.5 million deaths annually. Universal access to drug susceptibility testing (DST) has become a World Health Organization priority. We previously developed a software tool, Mykrobe predictor, which provided offline species identification and drug resistance predictions for M. tuberculosis from whole genome sequencing (WGS) data. Performance was insufficient to support the use of WGS as an alternative to conventional phenotype-based DST, due to mutation catalogue limitations. Here we present a new tool, Mykrobe, which provides the same functionality based on a new software implementation. Improvements include i) an updated mutation catalogue giving greater sensitivity to detect pyrazinamide resistance, ii) support for user-defined resistance catalogues, iii) improved identification of non-tuberculous mycobacterial species, and iv) an updated statistical model for Oxford Nanopore Technologies sequencing data. Mykrobe is released under MIT license at https://github.com/mykrobe-tools/mykrobe. We incorporate mutation catalogues from the CRyPTIC consortium et al. (2018) and from Walker et al. (2015), and make improvements based on performance on an initial set of 3206 and an independent set of 5845 M. tuberculosis Illumina sequences. To give estimates of error rates, we use a prospectively collected dataset of 4362 M. tuberculosis isolates. Using culture based DST as the reference, we estimate Mykrobe to be 100%, 95%, 82%, 99% sensitive and 99%, 100%, 99%, 99% specific for rifampicin, isoniazid, pyrazinamide and ethambutol resistance prediction respectively. We benchmark against four other tools on 10207 (=5845+4362) samples, and also show that Mykrobe gives concordant results with nanopore data. We measure the ability of Mykrobe-based DST to guide personalized therapeutic regimen design in the context of complex drug susceptibility profiles, showing 94% concordance of implied regimen with that driven by phenotypic DST, higher than all other benchmarked tools., ZI was funded by a Wellcome Trust/Royal Society Sir Henry Dale Fellowship, grant number 102541. MH was supported by Wellcome Trust/Newton Fund-MRC Collaborative Award [200205]; and Bill & Melinda Gates Foundation Trust [OPP1133541]. TMW is a Wellcome Trust Clinical Career Development Fellow, grant number 214560. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Published
2020
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36. Outbreak of multidrug-resistant tuberculosis in South Africa undetected by WHO-endorsed commercial tests: an observational study

Author

Bouke C. de Jong, Lufuno Razwiedani, Agathe Jouet, Jean-Charles Delvenne, Ndivhuho Agnes Makhado, Stefan Niemann, Léonie Goeminne, Fairouz Boutachkourt, Cyril Gaudin, Patrick Beckert, Maphoshane Nchabeleng, Gugu Maphalala, Emmanuel André, Mauro Faccin, Michel Delmée, Philip Supply, Claire Pinçon, Edith Matabane, Santé publique : épidémiologie et qualité des soins-EA 2694 (CERIM), Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), Laboratoire de cristallographie et RMN biologiques (LCRB - UMR 8015), Centre National de la Recherche Scientifique (CNRS)-Université Paris Descartes - Paris 5 (UPD5), Molecular Mycobacteriology Group, National Reference Center for Mycobacyeria, Fonds de la Recherche Scientifique (FNRS), Fonds de la Recherche Scientifique [FNRS], Centre d’Infection et d’Immunité de Lille (CIIL) - U1019 - UMR 8204 (CIIL), Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Department of Biomedical Sciences [Antwerp], Institute of Tropical Medicine [Antwerp] (ITM), Evaluation des technologies de santé et des pratiques médicales - ULR 2694 (METRICS), Université Paris Descartes - Paris 5 (UPD5)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204 (CIIL), Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Université de Lille-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur de Lille, and Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)

Subjects
Adult, Male, 0301 basic medicine, Tuberculosis, Genotyping Techniques, 030106 microbiology, Mutation, Missense, Drug resistance, Polymerase Chain Reaction, Sensitivity and Specificity, Disease Outbreaks, Mycobacterium tuberculosis, South Africa, Young Adult, 03 medical and health sciences, chemistry.chemical_compound, symbols.namesake, Gene Frequency, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Tuberculosis, Multidrug-Resistant, medicine, Humans, Diagnostic Errors, ComputingMilieux_MISCELLANEOUS, Sanger sequencing, biology, DNA-Directed RNA Polymerases, Sequence Analysis, DNA, Middle Aged, biology.organism_classification, rpoB, medicine.disease, Virology, 3. Good health, Multiple drug resistance, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Infectious Diseases, Molecular Diagnostic Techniques, chemistry, symbols, Female, Mutant Proteins, Human medicine, Bedaquiline, Rifampicin, medicine.drug
Abstract

Summary Background Global roll-out of rapid molecular assays is revolutionising the diagnosis of rifampicin resistance, predictive of multidrug-resistance, in tuberculosis. However, 30% of the multidrug-resistant (MDR) strains in an eSwatini study harboured the Ile491Phe mutation in the rpoB gene, which is associated with poor rifampicin-based treatment outcomes but is missed by commercial molecular assays or scored as susceptible by phenotypic drug-susceptibility testing deployed in South Africa. We evaluated the presence of Ile491Phe among South African tuberculosis isolates reported as isoniazid-monoresistant according to current national testing algorithms. Methods We screened records of 37 644 Mycobacterium tuberculosis positive cultures from four South African provinces, diagnosed at the National Health Laboratory Service–Dr George Mukhari Tertiary Laboratory, to identify isolates with rifampicin sensitivity and isoniazid resistance according to Xpert MTB/RIF, GenoType MTBDRplus, and BACTEC MGIT 960. Of 1823 isolates that met these criteria, 277 were randomly selected and screened for Ile491Phe with multiplex allele-specific PCR and Sanger sequencing of rpoB. Ile491Phe-positive strains (as well as 17 Ile491Phe-bearing isolates from the eSwatini study) were then tested by Deeplex-MycTB deep sequencing and whole-genome sequencing to evaluate their patterns of extensive resistance, transmission, and evolution. Findings Ile491Phe was identified in 37 (15%) of 249 samples with valid multiplex allele-specific PCR and sequencing results, thus reclassifying them as MDR. All 37 isolates were additionally identified as genotypically resistant to all first-line drugs by Deeplex-MycTB. Six of the South African isolates harboured four distinct mutations potentially associated with decreased bedaquiline sensitivity. Consistent with Deeplex-MycTB genotypic profiles, whole-genome sequencing revealed concurrent silent spread in South Africa of a MDR tuberculosis strain lineage extending from the eSwatini outbreak and at least another independently emerged Ile491Phe-bearing lineage. Whole-genome sequencing further suggested acquisition of mechanisms compensating for the Ile491Phe fitness cost, and of additional bedaquiline resistance following the introduction of this drug in South Africa. Interpretation A substantial number of MDR tuberculosis cases harbouring the Ile491Phe mutation in the rpoB gene in South Africa are missed by current diagnostic strategies, resulting in ineffective first-line treatment, continued amplification of drug resistance, and concurrent silent spread in the community. Funding VLIR-UOS, National Research Foundation (South Africa), and INNOVIRIS.

Published
2018
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37. Prevalence and drivers of false-positive rifampicin-resistant Xpert MTB/RIF results: a prospective observational study in Rwanda

Author

Faridath Massou, Patrick Migambi, Armand Van Deun, Dissou Affolabi, Corinne S Merle, Bertin Ushizimpumu, Esdras Belamo Niyigena, Jean Baptiste Mazarati, Leen Rigouts, Bouke C. de Jong, Conor J. Meehan, Emil Ivan, Philip Supply, Jules Mugabo Semahore, Willem Bram de Rijk, Tom Decroo, Gabriela Torrea, Yves Mucyo Habimana, Jean Claude Semuto Ngabonziza, Rwanda Biomedical Center (RBC), Institute of Tropical Medicine [Antwerp] (ITM), Universiteit Antwerpen [Antwerpen], Research Foundation - Flanders [Brussel] (FWO), Damien Foundation, University of Bradford, Laboratoire de Référence des Mycobactéries [Cotonou, Benin], Hôpital Centre LAZARET [Cotonou, Bénin], WHO Country Office [Kigali, Rwanda] (WHO), Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO), UNICEF/UNDP/World Bank/WHO Special Programme for Research and Training in Tropical Diseases (TDR), Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO)-UNICEF Headquarters-World Bank Group-United Nations Development Programme (UNDP), London School of Hygiene and Tropical Medicine (LSHTM), Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204 (CIIL), Centre National de la Recherche Scientifique (CNRS)-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Université de Lille-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), The European & Developing Countries Clinical Trials Partnership 2 programme, and Belgian Directorate General for Development Cooperation., Universiteit Antwerpen = University of Antwerpen [Antwerpen], UNICEF Headquarters-World Bank Group-United Nations Development Programme (UNDP)-Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO), Institut Pasteur de Lille, and Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Microbiology (medical), medicine.medical_specialty, Tuberculosis, [SDV]Life Sciences [q-bio], lcsh:QR1-502, Drug resistance, Microbiology, lcsh:Microbiology, 03 medical and health sciences, 0302 clinical medicine, Virology, Internal medicine, polycyclic compounds, Medicine, 030212 general & internal medicine, lcsh:R5-920, 0303 health sciences, 030306 microbiology, business.industry, Odds ratio, medicine.disease, bacterial infections and mycoses, 3. Good health, Clinical trial, Pre- and post-test probability, Infectious Diseases, Observational study, lcsh:Medicine (General), business, Rifampicin, Cohort study, medicine.drug
Abstract

Summary Background The Xpert MTB/RIF (Xpert) assay is used globally to rapidly diagnose tuberculosis and resistance to rifampicin. We investigated the frequency and predictors of false-positive findings of rifampicin resistance with Xpert. Methods We did a prospective, observational study of individuals who were enrolled in a Rwandan nationwide diagnostic cohort study (DIAMA trial; NCT03303963 ). We included patients identified to have rifampicin resistance on initial Xpert testing. We did a repeat Xpert assay and used rpoB Sanger and deep sequencing alongside phenotypic drug susceptibility testing (pDST) to ascertain final rifampicin susceptibility status, with any (hetero)resistant result overriding. We used multivariable logistic regression to assess predictors of false rifampicin resistance on initial Xpert testing, adjusted for HIV status, tuberculosis treatment history, initial Xpert semi-quantitative bacillary load, and initial Xpert probe. Findings Between May 4, 2017, and April 30, 2019, 175 people were identified with rifampicin resistance at initial Xpert testing, of whom 154 (88%) underwent repeat Xpert assay. 54 (35%) patients were confirmed as rifampicin resistant on repeat testing and 100 (65%) were not confirmed with resistance. After further testing and sequencing, 121 (79%) of 154 patients had a final confirmed status for rifampicin susceptibility. 57 (47%) of 121 patients were confirmed to have a false rifampicin resistance result and 64 (53%) had true rifampicin resistance. A high pretest probability of rifampicin resistance did not decrease the odds of false rifampicin resistance (adjusted odds ratio [aOR] 6·0, 95% CI 1·0–35·0, for new tuberculosis patients vs patients who needed retreatment). Ten (16%) of the 64 patients with true rifampicin resistance did not have confirmed rifampicin resistance on repeat Xpert testing, of whom four had heteroresistance. Of 63 patients with a very low bacillary load on Xpert testing, 54 (86%) were falsely diagnosed with rifampicin-resistant tuberculosis. Having a very low bacillary load on Xpert testing was strongly associated with false rifampicin resistance at the initial Xpert assay (aOR 63·6, 95% CI 9·9–410·4). Interpretation The Xpert testing algorithm should include an assessment of bacillary load and retesting in case rifampicin resistance is detected on a paucibacillary sputum sample. Only when rifampicin resistance has been confirmed on repeat testing should multidrug-resistant tuberculosis treatment be started. When rifampicin resistance has not been confirmed on repeat testing, we propose that patients should be given first-line anti-tuberculosis drugs and monitored closely during treatment, including by baseline culture, pDST, and further Xpert testing. Funding The European & Developing Countries Clinical Trials Partnership 2 programme, and Belgian Directorate General for Development Cooperation.

Published
2020
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38. MAC-INMV-SSR: a web application dedicated to genotyping members of Mycobacterium avium complex (MAC) including Mycobacterium avium subsp. paratuberculosis strains

Author

Franck Biet, Thierry Cochard, Maxime Branger, Philip Supply, Srinand Sreevatsan, Infectiologie et Santé Publique (UMR ISP), Université de Tours-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204 (CIIL), Centre National de la Recherche Scientifique (CNRS)-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Université de Lille-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Departments of Microbiology & Molecular Genetics, and of Pathobiology & Diagnostic Investigation [East Lansing, USA], Michigan State University [East Lansing], Michigan State University System-Michigan State University System, This work was partly funded by Johne's Disease Integrated Program, a NIFA funded program project., Université de Tours (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Centre National de la Recherche Scientifique (CNRS), Infectiologie Santé Publique (ISP-311), Institut National de la Recherche Agronomique (INRA)-Université de Tours, UR Infectiologie animale et Santé publique (UR IASP), Institut National de la Recherche Agronomique (INRA), Centre d’Infection et d’Immunité de Lille (CIIL) - U1019 - UMR 8204 (CIIL), Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), and Supply, Philip

Subjects
Genetic Markers, 0301 basic medicine, Microbiology (medical), Genotyping, Genotyping Techniques, MLSSR, 030106 microbiology, Paratuberculosis, Minisatellite Repeats, Computational biology, Multiple Loci VNTR Analysis, Microbiology, MAC complex, Database, 03 medical and health sciences, Tandem repeat, Genetics, medicine, Web application, Typing, [SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology, Molecular Biology, ComputingMilieux_MISCELLANEOUS, Ecology, Evolution, Behavior and Systematics, Internet, biology, business.industry, MLVA, Computational Biology, Mycobacterium avium Complex, biology.organism_classification, medicine.disease, 3. Good health, Mycobacterium avium subsp. paratuberculosis, Variable number tandem repeat, 030104 developmental biology, Infectious Diseases, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, business, Software, Microsatellite Repeats, Multilocus Sequence Typing, Mycobacterium
Abstract

International audience; Genotyping of Mycobacterium avium subsp. paratuberculosis (Map) is an indispensable tool for surveillance of this significant veterinary pathogen. For Map, multi-locus variable number tandem repeat analysis (MLVA) targeting mycobacterial interspersed repetitive units (MIRUs) and other variable number variable-number tandem repeats (VNTRs) was established using 8 markers. In the recent past this standard, portable, reproducible and discriminatory typing method has been frequently applied alone or in combinations with multi-locus short-sequence-repeat (MLSSR) sequencing. With the widespread use of these genotyping methods, standardization between laboratories needs to be managed, and knowledge of existing profiles and newly defined genotypes should be indexed and shared. To meet this need, a web application called "MAC-INMV-SSR database" was developed. This freely accessible service allows users to compare MLVA and MLSSR subtype data of their strains with those of existing reference strains analyzed with the same genotyping methods.

Published
2020
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39. From environmental bacteria to obligate pathogen: the study of adaptations enhancing the persistence of tuberculosis bacilli

Author

Christophe Guilhot, Roland Brosch, Catherine Astarie-Dequeker, Aideen C. Allen, Ali Hassan, Philip Supply, Wladimir Malaga, Céline Berrone, and Flavie Moreau

Subjects
Genetics, Experimental evolution, Tuberculosis, Obligate, biology, business.industry, Virulence, Human pathogen, biology.organism_classification, medicine.disease, Mycobacterium tuberculosis, Medicine, business, Pathogen, Mycobacterium
Abstract

The highly contagious human pathogen Mycobacterium tuberculosis is responsible for an estimated 1.5 million deaths each year. A major feature of M. tuberculosis is its unique capacity to survive within the host for decades. In contrast, the evolutionary early-branching rare tubercle bacilli Mycobacterium canettii, which is thought to have originated from the same pool of ancestors as M. tuberculosis, rarely causes tuberculosis (TB) in humans and has a reduced capacity to persist and cause disease in the mouse model. Our objectives are to identify the genetic adaptations which allow persistence of TB bacilli within the host, and to characterise their functional consequences. Using an experimental evolution strategy, we have shown that recurrent in vivo passaging of a M. canettii strain (for more than 2 years) allows clones to emerge as “persistent mutants” that have a greater ability to survive in the host, and gain the characteristics of classical M. tuberculosis strains. Several “persistent mutants” were selected and the persistence phenotype was confirmed in several mouse genetic backgrounds. Next, these mutants were subjected to extensive phenotypic characterisation and were found to have enhanced resistance to stress encountered during infection, and increased virulence in human monocyte-derived macrophages. Currently, the mutations responsible for these phenotypes are being characterised. Comparing the genetic differences between the parental M. canettii strain, the “persistent” M. canettii clones and M. tuberculosis will help identify the molecular mechanisms driving evolution from putative generalist mycobacteria, towards professional human pathogen.

Published
2019
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40. Z oonotic tuberculosis in humans assessed by next-generation sequencing: an 18-month nationwide study in Lebanon

Author

Claire Pinçon, Cyril Gaudin, Marwan Osman, Philip Supply, Christine Demanche, Mohamad Bachar Ismail, Monzer Hamze, Rayane Rafei, Salam El Achkar, Stéphanie Duthoy, Frédérique De Matos, Hiam Yaacoub, Biodiversité et fonctionnement du sol (BIOSOL), Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris Diderot - Paris 7 (UPD7)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204 (CIIL), Centre National de la Recherche Scientifique (CNRS)-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Université de Lille-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Centre de Recherche en Cancérologie Nantes-Angers (CRCNA), Centre Hospitalier Universitaire d'Angers (CHU Angers), PRES Université Nantes Angers Le Mans (UNAM)-PRES Université Nantes Angers Le Mans (UNAM)-Hôtel-Dieu de Nantes-Institut National de la Santé et de la Recherche Médicale (INSERM)-Hôpital Laennec-Centre National de la Recherche Scientifique (CNRS)-Faculté de Médecine d'Angers-Centre hospitalier universitaire de Nantes (CHU Nantes), Laboratoire Microbiologie Santé et Environnement - LMSE [Tripoli, Lebanon] (Faculté de Santé Publique), Université Libanaise-Ecole Doctorale des Sciences et de Technologie [Tripoli, Lebanon], Laboratoire de cristallographie et RMN biologiques (LCRB - UMR 8015), Université Paris Descartes - Paris 5 (UPD5)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Genoscreen, Evaluation des technologies de santé et des pratiques médicales - ULR 2694 (METRICS), Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), Centre AZM pour la Recherche en Biotechnologie et ses Applications, Université Libanaise, Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Centre National de la Recherche Scientifique (CNRS), Centre d’Infection et d’Immunité de Lille (CIIL) - U1019 - UMR 8204 (CIIL), Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Centre de Recherche en Cancérologie / Nantes - Angers (CRCNA), Centre hospitalier universitaire de Nantes (CHU Nantes)-Faculté de Médecine d'Angers-Centre Hospitalier Universitaire d'Angers (CHU Angers), PRES Université Nantes Angers Le Mans (UNAM)-PRES Université Nantes Angers Le Mans (UNAM)-Centre National de la Recherche Scientifique (CNRS)-Hôpital Laennec-Institut National de la Santé et de la Recherche Médicale (INSERM)-Hôtel-Dieu de Nantes, Centre National de la Recherche Scientifique (CNRS)-Université Paris Descartes - Paris 5 (UPD5), and Santé publique : épidémiologie et qualité des soins-EA 2694 (CERIM)

Subjects
Pulmonary and Respiratory Medicine, 0303 health sciences, International call, Tuberculosis, 030306 microbiology, business.industry, 030231 tropical medicine, MEDLINE, medicine.disease, 3. Good health, 03 medical and health sciences, 0302 clinical medicine, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Environmental health, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Income country, Medicine, business, Bit (key), ComputingMilieux_MISCELLANEOUS
Abstract

International audience; The World Health Organization (WHO) and other international organisations, including the Food and Agriculture Organization of the United Nations, the World Organisation for Animal Health and the International Union Against Tuberculosis and Lung Disease recently called for formally assessing and (re)prioritising the burden of zoonotic tuberculosis (TB) in people, due to Mycobacterium bovis [1, 2]. Its global contribution to human TB, otherwise principally caused by Mycobacterium tuberculosis, might be underestimated [2]. Nationally representative prevalence data are virtually non-existent on continents with the highest presumed burdens, i.e. in Africa and Asia [3]. In addition to causing hard-to-diagnose extrapulmonary TB more frequently, M. bovis is naturally resistant to pyrazinamide [4], a crucial drug for the standard short-course anti-TB therapy. Due to reliability issues, phenotypic susceptibility to pyrazinamide is often not tested [5]. The most commonly used phenotypic and molecular diagnostics, including the WHO-endorsed GeneXpert MTB/RIF test (Cepheid, Sunnyvale, CA, USA), do not differentiate M. bovis from M. tuberculosis [1]. Thus, M. bovis-infected patients may receive inadequate treatment, risking poorer outcomes [6]. Underdiagnosis in people also implies the existence of undetected animal and food sources and zoonotic risks escaping common TB control measures [1, 2]. In Europe, patients with M. bovis infection are often African-or southern Mediterranean-born, suggesting regional endemicity [6, 7]. We determined the prevalence of M. bovis-caused TB in a survey including all TB patients reported to the national TB programme over an 18-month period in Lebanon. In addition to its national population and >1.5 million Syrian and Palestinian refugees, this Mediterranean country hosts large numbers of migrant workers from Africa and Asia [8]. Many are from Ethiopia [8], where proportions of extrapulmonary TB and M. bovis-caused disease among TB patients apparently culminate, reaching ∼30% [9] and 15-30% (in focal studies; [10]), respectively. We used a novel targeted next-generation sequencing-based assay for extensive drug resistance detection, including resistance to pyrazinamide, and genotypic differentiation between M. bovis and M. tuberculosis [11]. This survey was approved by the Azm Center/Lebanese University ethical committee (document CE-EDST-3-2016). Clinical samples were collected from all 1104 different TB patients with presumption of pulmonary or extrapulmonary TB, based on the presence of symptoms and prior tuberculin skin testing or radiological examination in local hospitals for a number of patients, and reported to all national anti-TB centres between June 1, 2016 and November 31, 2017. All of these 1104 patients were tested by at least one of the following assays: solid (Lowenstein-Jensen) and/or liquid (BBL MGIT; Beckton Dickinson, Franklin Lakes, NJ, USA) culturing, GeneXpert MTB/RIF on sputum, and Anyplex MTB/NTM Real-time (Seegene, Seoul, Republic of Korea) on sputum or culture on solid or liquid medium. Out of these 1104, 417 were confirmed as TB positive by GeneXpert and/or Anyplex. Among these 417 patients, 354 were culture positive. Among the 354 corresponding patients, 325 were new TB patients, 22 had a previous TB history, while TB history information was unavailable for seven patients. Available DNA extracts, obtained from 348 out of 354 primary cultures by using MasterPure™ DNA Purification Kit (Epicentre, Illumina, Madison, WI, USA), were subjected to targeted sequencing, more @ERSpublications In response to recent international calls, this study reveals the nationally representative prevalence of zoonotic tuberculosis in people in a non-high income country, highlighting the need for appropriate diagnostics and treatment of these patients http://bit.ly/2l3ydDh

Published
2019
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41. Whole genome sequencing of Mycobacterium tuberculosis: current standards and open issues

Author

Jennifer L. Guthrie, Sebastien Gagneux, Tim H. Heupink, Timothy M Walker, Annelies Van Rie, Philip Ashton, Maha R. Farhat, Daniela Brites, Galo A. Goig, Lennert Verboven, Dick van Soolingen, Christian Utpatel, Elisa Tagliani, Robin M. Warren, Qian Gao, Viola Dreyer, Philip Supply, Thomas Kohl, Fabrizio Menardo, Yanlin Zhao, Anzaan Dippenaar, Leen Rigouts, Andrea M. Cabibbe, Kris Laukens, Qingyun Liu, Marco Schito, Matteo Zignol, Margaretha de Vos, Iñaki Comas, Matthew Ezewudo, Stefan Niemann, Chloé Loiseau, Timothy C. Rodwell, Anita Suresh, Boatema Ofori-Anyinam, Daniela Maria Cirillo, Yang Zhou, Jennifer L. Gardy, Bouke C. de Jong, Conor J. Meehan, Paolo Miotto, Institute of Tropical Medicine [Antwerp] (ITM), Instituto de biomedicina [Valencia] (IBV), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Forschungszentrum Borstel - Research Center Borstel, German Center for Infection Research - Partner Site Hamburg-Lübeck-Borstel-Riems, German Centre for Infection Research (DZIF), Universiteit Antwerpen [Antwerpen], Stellenbosch University, Critical Path Institute [Tucson, AZ], Harvard Medical School [Boston] (HMS), Massachusetts General Hospital [Boston], University of British Columbia (UBC), IRCCS San Raffaele Scientific Institute [Milan, Italie], Center for Global Health Security and Diplomacy [Ottawa] (CGHSD), Food and Drugs Authority [Accra, Ghana] (FDA Ghana), Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204 (CIIL), Centre National de la Recherche Scientifique (CNRS)-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Université de Lille-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Foundation for Innovative New Diagnostics (FIND), National Institute for Public Health and the Environment [Bilthoven] (RIVM), Chinese Center for Disease Control and Prevention, University of Oxford [Oxford], Swiss Tropical and Public Health Institute [Basel], University of Basel (Unibas), Fudan University [Shanghai], John Radcliffe Hospital [Oxford University Hospital], Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO), C.J.M., B.O.-A., L.R. and B.C.d.J. are supported by a European Research Council grant (INTERRUPTB, no. 311725). I.C. and G.A.G. are supported by a European Research Council grant (TB-ACCELERATE, no. 638553). T.C.R. receives salary support from the not-for-profit organization Foundation for Innovative New Diagnostics (the terms of this arrangement have been reviewed and approved by the University of California, San Diego). T.M.W. is an NIHR Academic Clinical Lecturer. J.L.G. and J.G. receive funding from the University of British Columbia, Vancouver, Canada. T.A.K., C.U., V.D. and S.N. receive funding from the German Center for Infection Research (DZIF) and are funded by the Deutsche Forschungsgemeinschaft (German Research Foundation) under Germany’s Excellence Strategy (EXC 22167–390884018). L.V., T.H.H. and A.V.R. are funded by FWO Odysseus G0F8316N. M.R.F. is supported by the US National Institutes of Health BD2K K01 (MRF ES026835). P.S. is supported by the Agence Nationale de la Recherche (ANR-16-CE35-0009)., ANR-16-CE35-0009,TBemerg,Naissance d'un tueur: facteurs génétiques et adaptations métaboliques impliquées dans l'émergence des bacilles tuberculeux épidémiques(2016), European Project: 311725,EC:FP7:ERC,ERC-2012-StG_20111109,INTERRUPTB(2013), European Project: 638553,H2020,ERC-2014-STG,TB-ACCELERATE(2015), Universiteit Antwerpen = University of Antwerpen [Antwerpen], Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Centre National de la Recherche Scientifique (CNRS), and University of Oxford

Subjects
Tuberculosis, Best practice, Sequencing data, Harmonization, Biology, Microbiology, Mycobacterium tuberculosis, 03 medical and health sciences, Public health surveillance, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Drug Resistance, Bacterial, medicine, Humans, Phylogeny, Whole genome sequencing, Computer. Automation, 0303 health sciences, Molecular Epidemiology, General Immunology and Microbiology, Whole Genome Sequencing, 030306 microbiology, Computational Biology, medicine.disease, biology.organism_classification, Data science, 3. Good health, Infectious Diseases, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Molecular Diagnostic Techniques, Practice Guidelines as Topic, Human medicine
Abstract

International audience; Whole genome sequencing (WGS) of Mycobacterium tuberculosis has rapidly progressed from a research tool to a clinical application for the diagnosis and management of tuberculosis and in public health surveillance. This development has been facilitated by drastic drops in cost, advances in technology and concerted efforts to translate sequencing data into actionable information. There is, however, a risk that, in the absence of a consensus and international standards, the widespread use of WGS technology may result in data and processes that lack harmonization, comparability and validation. In this Review, we outline the current landscape of WGS pipelines and applications, and set out best practices for M. tuberculosis WGS, including standards for bioinformatics pipelines, curated repositories of resistance-causing variants, phylogenetic analyses, quality control and standardized reporting.

Published
2019
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42. How well do routine molecular diagnostics detect rifampicin heteroresistance in Mycobacterium tuberculosis?

Author

Philip Supply, Julian Gonzalez-Martin, Bouke C. de Jong, Cyril Gaudin, Frank Cobelens, Kamela C. S. Ng, and Leen Rigouts

Subjects
0303 health sciences, Tuberculosis, biology, 030306 microbiology, business.industry, Drug susceptibility, Rifampicin resistance, Molecular diagnostics, biology.organism_classification, medicine.disease, bacterial infections and mycoses, Virology, 3. Good health, Mycobacterium tuberculosis, 03 medical and health sciences, Genotype, medicine, polycyclic compounds, Mutation type, business, Rifampicin, 030304 developmental biology, medicine.drug
Abstract

Rifampicin heteroresistance – where rifampicin-resistant and -susceptible tuberculosis (TB) bacilli co-exist – may result in failed standard TB treatment and potential spread of rifampicin-resistant strains. Detection of rifampicin heteroresistance in routine rapid diagnostic tests (RDTs) allows for patients to receive prompt and effective multidrug-resistant-TB treatment, and may improve rifampicin-resistant TB control.The limit of detection (LOD) of rifampicin heteroresistance for phenotypic drug susceptibility testing by the proportion method is 1%, yet is insufficiently documented for RDTs. We therefore aimed to determine, for the four RDTs (XpertMTB/RIF, XpertMTB/RIF Ultra, GenoTypeMTBDRplusv2.0, and GenoscholarNTM+MDRTBII), the LOD per probe and mutation, validated by colony-forming-unit-counting and targeted deep sequencing (Deeplex-MycTB).We selected one rifampicin-susceptible and four rifampicin-resistant strains, with mutation D435V, H445D, H445Y, and S450L respectively, mixed them in various proportions in triplicate, tested them with each RDT, and determined the LODs per mutation type. Deeplex-MycTB revealed concordant proportions of the minority resistant variants in the mixtures. The Deeplex-MycTB-validated-LODs ranged from 20-80% for XpertMTB/RIF, 20-70% for Xpert Ultra, 5-10% for GenoTypeMTBDRplusv2.0, and 1-10% for GenoscholarNTM+MTBII for the different mutations.Deeplex-MycTB, GenoTypeMTBDRplusv2.0, and GenoscholarNTM+MDRTBII, provide explicit information on rifampicin heteroresistance for the most frequently detected mutations. Classic Xpert and Ultra report rifampicin heteroresistance as rifampicin resistance, while Ultra may denote rifampicin heteroresistance through ‘mixed patterns’ of wild-type and mutant melt probe melt peak temperatures.Overall, our findings inform end-users that the threshold for reporting resistance in case of rifampicin heteroresistance is the highest for Classic Xpert and Ultra, to resolve phenotypic and genotypic discordant rifampicin-resistant TB results.

Published
2019
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43. An Outpatient Clinic as a Potential Site of Transmission for an Outbreak of New Delhi Metallo-β-Lactamase–producing Klebsiella pneumoniae Sequence Type 716: A Study Using Whole-genome Sequencing

Author

Maria Angeles Argudín, Jill Dombrecht, Baudouin Byl, Youri Glupczynski, Ariane Deplano, Olivier Denis, Julien Coussement, Sandrine Roisin, Magali Dodémont, Lorenzo L. Filippin, Katrien De Bruyne, Amélie Heinrichs, Te-Din Huang, Ricardo De Mendonça, Philip Supply, Department Infections Diseases, Université libre de Bruxelles (ULB), Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204 (CIIL), Centre National de la Recherche Scientifique (CNRS)-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Université de Lille-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Cliniques universitaires UCL de Mont-Godinne 5530 Yvoir, Institut Pasteur de Lille, and Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Microbiologie et protistologie [parasitologie hum. et anim.], 0301 basic medicine, Microbiology (medical), medicine.medical_specialty, Klebsiella pneumoniae, 030106 microbiology, Prevalence, Microbial Sensitivity Tests, Drug resistance, Ambulatory Care Facilities, beta-Lactamases, Disease Outbreaks, carbapenemase, 03 medical and health sciences, 0302 clinical medicine, ambulatory care, Ambulatory care, Internal medicine, Acute care, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Drug Resistance, Bacterial, medicine, Cluster Analysis, Humans, Infection control, Outpatient clinic, 030212 general & internal medicine, Pathologie maladies infectieuses, whole-genome MLST, ComputingMilieux_MISCELLANEOUS, Cross Infection, Whole Genome Sequencing, biology, business.industry, Computational Biology, Outbreak, Molecular Sequence Annotation, biology.organism_classification, infection control, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Klebsiella Infections, 3. Good health, Microbiologie et protistologie [entomologie,phytoparasitolog.], nosocomial outbreak, Infectious Diseases, Microbiologie et protistologie [bacteriol.virolog.mycolog.], business, Genome, Bacterial
Abstract

Background The incidence of nosocomial infections due to carbapenem-resistant Klebsiella pneumoniae is increasing worldwide. Whole-genome sequencing (WGS) can help elucidate the transmission route of nosocomial pathogens. Methods We combined WGS and epidemiological data to analyze an outbreak of New Delhi metallo-β-lactamase (NDM)-producing K. pneumoniae that occurred in 2 Belgian hospitals situated about 50 miles apart. We characterized 74 NDM-producing K. pneumoniae isolates (9 from hospital A, 24 from hospital B, and 41 contemporary isolates from 15 other Belgian hospitals) using pulsed-field gel electrophoresis and WGS. Results A K. pneumoniae sequence type 716 clone was identified as being responsible for the outbreak with all 9 strains from hospital A and 20 of 24 from hospital B sharing a unique pulsotype and being clustered together at WGS (compared with 1 of 41 isolates from other Belgian hospitals). We identified the outpatient clinic of hospital B as the probable bridging site between the hospitals after combining epidemiological, phylogenetic, and resistome data. We also identified the patient who probably caused the transmission. In fact, all but 1 strain from hospital A carried a Tn1331-like transposon, whereas none of the hospital B isolates did. The patient from hospital A who did not have the Tn1331-like transposon was treated at the outpatient clinic of hospital B on the same day as the first NDM-producing K. pneumoniae-positive patient from hospital B. Conclusions The results from our WGS-guided investigation highlight the importance of implementing adequate infection control measures in outpatient settings, especially when healthcare delivery moves from acute care facilities to outpatient clinics., SCOPUS: ar.j, info:eu-repo/semantics/published

Published
2019
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44. Drug-Resistant Tuberculosis, Lebanon, 2016 - 2017

Author

Claire Pinçon, Monzer Hamze, Marwan Osman, Alberto Trovato, Philip Supply, Cyril Gaudin, Christine Demanche, Mohamad Bachar Ismail, Rayane Rafei, Salam El Achkar, Daniela Maria Cirillo, Hiam Yaacoub, Frédérique De Matos, Stéphanie Duthoy, CHU Lille, CNRS, Inserm, Institut Pasteur de Lille, Université de Lille, Centre d'Infection et d'Immunité de Lille (CIIL) - U1019 - UMR 9017, Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204 [CIIL], METRICS : Evaluation des technologies de santé et des pratiques médicales - ULR 2694, University of Tripoli - University Al Fateh, Evaluation des technologies de santé et des pratiques médicales - ULR 2694 [METRICS], Genoscreen [Lille], IRCCS Istituto Nazionale dei Tumori [Milano], Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204 (CIIL), Centre National de la Recherche Scientifique (CNRS)-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Université de Lille-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Université Libanaise, IRCCS San Raffaele Scientific Institute [Milan, Italie], Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Centre National de la Recherche Scientifique (CNRS), and Supply, Philip

Subjects
Male, Epidemiology, Antitubercular Agents, lcsh:Medicine, Drug resistance, Minisatellite Repeats, 0302 clinical medicine, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Drug Resistance, Multiple, Bacterial, Tuberculosis, Multidrug-Resistant, MDR, 030212 general & internal medicine, DNA sequencing, Lebanon, bacteria, Drug-Resistant Tuberculosis, Lebanon, 2016–2017, health care economics and organizations, Dispatch, food and beverages, TB, Tuberculosis, XDR, antimicrobial resistance, asylum seekers, drug resistance, migrant workers, refugees, survey, tuberculosis and other mycobacteria, whole-genome sequencing, Middle Aged, 3. Good health, Infectious Diseases, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, population characteristics, Female, Microbiology (medical), Adult, Genotype, Refugee, 030231 tropical medicine, education, Microbial Sensitivity Tests, History, 21st Century, lcsh:Infectious and parasitic diseases, 03 medical and health sciences, Young Adult, Antibiotic resistance, Environmental health, medicine, Humans, lcsh:RC109-216, business.industry, Drug resistant tuberculosis, Migrant workers, lcsh:R, fungi, Mycobacterium tuberculosis, medicine.disease, [SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie, Genes, Bacterial, Mutation, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Treatment decision making, business
Abstract

International audience; In a 12-month nationwide study on the prevalence of drug-resistant tuberculosis (TB) in Lebanon, we identified 3 multidrug-resistant cases and 3 extensively drug-resistant TB cases in refugees, migrants, and 1 Lebanon resident. Enhanced diagnostics, particularly in major destinations for refugees, asylum seekers, and migrant workers, can inform treatment decisions and may help prevent the spread of drug-resistant TB.

Published
2019
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45. Multidrug-resistant tuberculosis outbreak in South Africa – Authors' reply

Author

Ndivhuho A. Makhado, Bouke C. de Jong, Maphoshane Nchabeleng, Philip Supply, Emmanuel André, Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204 (CIIL), Centre National de la Recherche Scientifique (CNRS)-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Université de Lille-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Department of Biomedical Sciences [Antwerp], Institute of Tropical Medicine [Antwerp] (ITM), Institut Pasteur de Lille, and Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0303 health sciences, Tuberculosis, 030306 microbiology, business.industry, Outbreak, medicine.disease, Virology, Multiple drug resistance, 03 medical and health sciences, 0302 clinical medicine, Infectious Diseases, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Medicine, 030212 general & internal medicine, business, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2019
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46. Pan-genome multilocus sequence typing and outbreak-specific reference-based single nucleotide polymorphism analysis to resolve two concurrent Staphylococcus aureus outbreaks in neonatal services

Author

K. Van Vaerenbergh, O. Denis, R. De Mendonça, Philip Supply, J. Bellon, B. Byl, C. Gaudin, Sandrine Roisin, Hannes Pouseele, and K. De Bruyne

Subjects
0301 basic medicine, Microbiology (medical), Staphylococcus aureus, 030106 microbiology, Sequence assembly, Single-nucleotide polymorphism, Biology, Staphylococcal infections, Polymorphism, Single Nucleotide, Disease Outbreaks, 03 medical and health sciences, 0302 clinical medicine, Belgium, medicine, Humans, 030212 general & internal medicine, First episode, Whole genome sequencing, Genetics, Cross Infection, Molecular Epidemiology, Molecular epidemiology, Infant, Newborn, Outbreak, General Medicine, Staphylococcal Infections, medicine.disease, Hospitals, Infectious Diseases, Multilocus sequence typing, Genome, Bacterial, Multilocus Sequence Typing
Abstract

We used a two-step whole genome sequencing analysis for resolving two concurrent outbreaks in two neonatal services in Belgium, caused by exfoliative toxin A-encoding-gene-positive (eta+) methicillin-susceptible Staphylococcus aureus with an otherwise sporadic spa-type t209 (ST-109). Outbreak A involved 19 neonates and one healthcare worker in a Brussels hospital from May 2011 to October 2013. After a first episode interrupted by decolonization procedures applied over 7 months, the outbreak resumed concomitantly with the onset of outbreak B in a hospital in Asse, comprising 11 neonates and one healthcare worker from mid-2012 to January 2013. Pan-genome multilocus sequence typing, defined on the basis of 42 core and accessory reference genomes, and single-nucleotide polymorphisms mapped on an outbreak-specific de novo assembly were used to compare 28 available outbreak isolates and 19 eta+/spa-type t209 isolates identified by routine or nationwide surveillance. Pan-genome multilocus sequence typing showed that the outbreaks were caused by independent clones not closely related to any of the surveillance isolates. Isolates from only ten cases with overlapping stays in outbreak A, including four pairs of twins, showed no or only a single nucleotide polymorphism variation, indicating limited sequential transmission. Detection of larger genomic variation, even from the start of the outbreak, pointed to sporadic seeding from a pre-existing exogenous source, which persisted throughout the whole course of outbreak A. Whole genome sequencing analysis can provide unique fine-tuned insights into transmission pathways of complex outbreaks even at their inception, which, with timely use, could valuably guide efforts for early source identification.

Published
2016
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47. Precision tuberculosis control by genome sequencing: Benefit and challenges of a new standard

Author

Philip Supply, Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204 (CIIL), Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Université de Lille-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur de Lille, and Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)

Subjects
0301 basic medicine, 030106 microbiology, MEDLINE, General Medicine, Computational biology, Genomics, Mycobacterium tuberculosis, Biology, Precision medicine, Genome, Polymorphism, Single Nucleotide, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, General Biochemistry, Genetics and Molecular Biology, DNA sequencing, 3. Good health, 03 medical and health sciences, 030104 developmental biology, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Commentary, Humans, Tuberculosis, Tuberculosis control, Precision Medicine, Genome, Bacterial, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2018
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48. Changing patterns of human migrations shaped the global population structure of Mycobacterium tuberculosis in France

Author

Ghislaine Blasquez, Charlotte Genestet, Gérard Carret, Catherine Pichat, Isabelle Fredenucci, Florence Ader, Sandrine Boisset, Anne Carricajo, Jean-Pierre Flandrois, Jean-Philippe Rasigade, Thierry Wirth, Maxime Barbier, Gerard Lina, Michèle Pérouse de Montclos, Anne-Sophie Ronnaux-Baron, Philip Supply, Christine Godin-Benhaim, Véronique Jacomo, Oana Dumitrescu, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Pathogénie des Staphylocoques – Staphylococcal Pathogenesis (StaPath), Centre International de Recherche en Infectiologie - UMR (CIRI), Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Institut des Agents Infectieux [Lyon] (IAI), Hospices Civils de Lyon (HCL), Comité Départemental d’Hygiène Sociale - CLAT69 [Lyon), Agence régionale de santé Auvergne Rhône Alpes (ARS), Laboratoire de Bactériologie, CHU Grenoble-Université Joseph Fourier - Grenoble 1 (UJF), Unité de contrôle infectieux [CHU Saint Etienne], Centre Hospitalier Universitaire de Saint-Etienne (CHU de Saint-Etienne), Biomnis Laboratory, Laboratoire des pathogènes émergents -- Emerging Pathogens Laboratory (LPE-Fondation Mérieux), Département PEGASE [LBBE] (PEGASE), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Pathogenèse des légionelles- Legionella pathogenesis (LegioPath), Service de Maladies Infectieuses et Tropicales [Hôpital de la Croix-Rousse - HCL], Hôpital de la Croix-Rousse [CHU - HCL], Hospices Civils de Lyon (HCL)-Hospices Civils de Lyon (HCL), Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204 (CIIL), Centre National de la Recherche Scientifique (CNRS)-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Université de Lille-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Muséum national d'Histoire naturelle (MNHN)-École Pratique des Hautes Études (EPHE), Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université Joseph Fourier - Grenoble 1 (UJF)-CHU Grenoble, Centre Hospitalier Universitaire de Saint-Etienne [CHU Saint-Etienne] (CHU ST-E), Institut Pasteur de Lille, and Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0301 basic medicine, DNA, Bacterial, Tuberculosis, Human Migration, Population, lcsh:Medicine, Datasets as Topic, Minisatellite Repeats, Article, Mycobacterium tuberculosis, 03 medical and health sciences, Global population, Africa, Northern, medicine, Humans, education, Tuberculosis incidence, lcsh:Science, Retrospective Studies, education.field_of_study, Multidisciplinary, biology, Human migration, business.industry, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Incidence, lcsh:R, biology.organism_classification, medicine.disease, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 3. Good health, Phylogeography, 030104 developmental biology, Minisatellite, Geography, Cross-Sectional Studies, Haplotypes, Evolutionary biology, lcsh:Q, France, business, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract

Mycobacterium tuberculosis (Mtb) exhibits a structured phylogeographic distribution worldwide linked with human migrations. We sought to infer how the interactions between distinct human populations shape the global population structure of Mtb on a regional scale. We applied the recently described timescaled haplotypic density (THD) technique on 638 minisatellite-based Mtb genotypes from French tuberculosis patients. THD with a long-term (200 y) timescale indicated that Mtb population in France had been mostly influenced by interactions with Eastern and Southern Europe and, to a lesser extent, Northern and Middle Africa, consistent with historical migrations favored by geographic proximity or commercial exchanges with former French colonies. Restricting the timescale to 20 y, THD identified a sustained influence of Northern Africa, but not Europe where tuberculosis incidence decreased sharply. Evolving interactions between human populations, thus, measurably influence the local population structure of Mtb. Relevant information on such interactions can be inferred using THD from Mtb genotypes.

Published
2018
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49. Set-up and validation of mycobacterial interspersed repetitive unit-variable number of tandem repeat (MIRU-VNTR) analysis of Mycobacterium tuberculosis using BioNumerics software

Author

Erik Svensson, Philip Supply, Mathias Klok Pedersen, Dorte Bek Folkvardsen, Aase Bengaard Andersen, Troels Lillebaek, Erik Michael Rasmussen, Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204 (CIIL), Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Université de Lille-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur de Lille, and Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)

Subjects
0301 basic medicine, Bacterial Diseases, Computer science, lcsh:Medicine, Artificial Gene Amplification and Extension, Minisatellite Repeats, Polymerase Chain Reaction, Capillary Electrophoresis, law.invention, Geographical Locations, chemistry.chemical_compound, Software, law, Medicine and Health Sciences, Genome Sequencing, lcsh:Science, Polymerase chain reaction, ComputingMilieux_MISCELLANEOUS, Molecular Epidemiology, Multidisciplinary, biology, Multi-drug-resistant tuberculosis, Multi-Drug-Resistant Tuberculosis, 3. Good health, Bacterial Typing Techniques, Actinobacteria, Europe, Infectious Diseases, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Variable number, Research Article, Genotyping, Genotype, Concordance, 030106 microbiology, Computational biology, Research and Analysis Methods, DNA sequencing, Set (abstract data type), Mycobacterium tuberculosis, 03 medical and health sciences, Electrophoretic Techniques, Tandem repeat, medicine, Tuberculosis, Humans, Allele, Molecular Biology Techniques, Sequencing Techniques, Molecular Biology, Alleles, Bacteria, business.industry, lcsh:R, Organisms, Biology and Life Sciences, medicine.disease, biology.organism_classification, Tropical Diseases, DNA Fingerprinting, chemistry, People and Places, lcsh:Q, business, DNA
Abstract

The objective was to describe and validate a new and alternative software procedure for 24-locus mycobacterial interspersed repetitive unit-variable number-tandem repeat (MIRU-VNTR) typing of Mycobacterium tuberculosis (Mtb) based on the multipurpose BioNumerics software. DNA from randomly selected isolates of Mtb from two European laboratories, including external control samples for MIRU-VNTR typing, were analysed. Samples were genotyped using the commercial 24-locus VNTR typing kit from GenoScreen. The PCR amplified fragments were separated by capillary electrophoresis. For the subsequent analyses, the currently used software GeneMapper was compared with BioNumerics. The endpoint was the level of concordance when comparing genotyping results obtained from BioNumerics with results obtained from GeneMapper and the ECDC proficiency study reference results. Also, the number of necessary manual standard size corrections and allele assignments in the two different software methods were compared. In total, 272 DNA samples, including the ECDC proficiency panel, were analysed. For all samples, there were 100% concordance of results. For a randomly selected set of 96 samples the numbers of manual corrections needed for size standards were 199 with GeneMapper versus zero for BioNumerics. The numbers of manual corrections for allele assignments were 122 with GeneMapper versus 16 with BioNumerics. In conclusion, we have validated the multipurpose software BioNumerics for standard 24-locus MIRU-VNTR typing and the software shows promising benefits in terms of simplification and minimization of hand-on time.

Published
2018
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50. Evolutionary history and global spread of the Mycobacterium tuberculosis Beijing lineage

Author

Sabine Rüsch-Gerdes, Hans P eter Beck, Vladyslav Nikolayevskyy, Irina Kontsevaya, Petras Stakenas, Kadri Toit, Shinji Maeda, Eman Aleksic, Marie Ballif, Stefano Mona, Troels Lillebaek, Maryline Bonnet, Caroline Allix-Béguec, Sophie Lecher, Robin M. Warren, Isdore Chola Shamputa, Francesca Barletta, Isolina Campos-Herrero, Wei wei Jiao, Thomas Kohl, Suzanne M. Crowe, Ewa Augustynowicz-Kopeć, Solomon Ghebremichael, Branislava Savic, Francis Varaine, Dragana Vuković, Camille Blin, Annick Antierens, Li Hwei Sng, Maryse Fauville-Dufaux, Céline Wahl, Thierry Wirth, Stefan Niemann, Eve Willery, Helen Cox, Valeriu Crudu, Emanuele Borroni, Sebastien Gagneux, Philip Supply, Sven Hoffner, Adong Shen, Stobdan Kalon, Michael Rasmussen, Francis Drobniewski, Igor Mokrousov, Michael G. B. Blum, Madeleine Hanekom, Sofía Samper, Matthias Merker, Clifton E. Barry, Nicolas Duforet-Frebourg, Roland Diel, Nalin Rastogi, Daniela Maria Cirillo, Elisabeth Sanchez-Padilla, Molecular Mycobacteriology, Research Center Borstel - Leibniz Lung Center [Germany], Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Biologie Intégrative des Population, Evolution Moléculaire, École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), Biologie Computationnelle et Mathématique (TIMC-IMAG-BCM), Techniques de l'Ingénierie Médicale et de la Complexité - Informatique, Mathématiques et Applications, Grenoble - UMR 5525 (TIMC-IMAG), Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204 (CIIL), Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Centre National de la Recherche Scientifique (CNRS), National Reference Center for Mycobacteria, Institut Pasteur de Saint-Pétersbourg, Réseau International des Instituts Pasteur (RIIP), Centre for Biomedical Research, Burnet Institute [Melbourne, Victoria], genoscreen, GenoScreen, Medical Department, Médecins sans Frontières [Genève] (MSF), Department of Microbiology, National Tuberculosis and Lung Diseases Research Institute, Institute of Social and Preventive Medicine, Universität Bern [Bern] (UNIBE), Instituto de Medicina Tropical Alexander von Humboldt, Molecular Epidemiology Unit–Tuberculosis, Instituto de Medicina Tropical 'Alexander von Humboldt' (IMT AvH), Universidad Peruana Cayetano Heredia (UPCH)-Universidad Peruana Cayetano Heredia (UPCH), Medical Parasitology and Infection Biology [Basel, Suisse] (MPI), Swiss Tropical and Public Health Institute [Basel], Laboratoire de Recherche en Informatique d'Amiens (LaRIA), Université de Picardie Jules Verne (UPJV)-Centre National de la Recherche Scientifique (CNRS), Epicentre [Paris] [Médecins Sans Frontières], Emerging Bacterial Pathogen Unit, San Raffaele Scientific Institute, hospital Universitario de Gran Canaria Dr Negrin, Macfarlane Burnet Institute for Medical Research, Laboratoire Jean Alexandre Dieudonné (LJAD), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), PHE National Mycobacterial Reference Laboratory and Clinical TB and HIV Group, Queen Mary's School of Medicine and Dentistry, Division of Infectious Diseases, Imperial College London, Centre national de Référence et Laboratoire Tuberculose et Mycobactéries = National Reference Centre of Tuberculosis and Mycobacteria [Brussels] (CNR), Institut Scientifique de Santé Publique [Belgique] - Scientific Institute of Public Health [Belgium] (WIV-ISP), Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), MRC National Institute for Medical Research, Department of Preparedness, Swedish Institute for Infectious Disease Control, Faculty of Medicine and Health Sciences, stellen, Key Laboratory of Major Diseases in Children, Beijing Children's Hospital affiliated to Capital Medical University-Beijing Pediatric Research Institute-Chine - Ministry of Education, Samara Oblast TB Service, Research institute of Tuberculosis, Anti-tuberculosis Association, Institut Pasteur de la Guadeloupe, LAboratoire de Recherche en Mécanique Appliquée (LARMAUR), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS), Mycobacteriology Unit, Prince Leopold Institute of Tropical Medicine, Microbiology Unit, Tropical Diseases Research Centre [Zambia] (TDRC), Alcatel-Thalès III-V lab (III-V Lab), THALES [France]-ALCATEL, Central Tuberculosis Laboratory, Singapore General Hospital, Medecins Sans Frontieres (Medecins Sans Frontieres), Médecins Sans Frontières, DTU Fotonik - Department of Photonics Engineering, Danmarks Tekniske Universitet = Technical University of Denmark (DTU), molecular biology and human genetics, Stell, Molecular Mycobacteriology Group, National Reference Center for Mycobacyeria, Origine, structure et évolution de la biodiversité (OSEB), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), We acknowledge J. Peh for her assistance and support in the study andI. Comas for statistical advice. Parts of this work have been supported by grantsfrom the European Community’s Seventh Framework Programme (FP7/2007-2013) under grant agreement 278864 in the framework of the European UnionPathoNGenTrace project and grant agreement 223681 in the framework of theTB-PAN-NET project. We also thank Action Transversale du Muséum Nationald’Histoire Naturelle ‘Les Microorganismes, Acteurs Clés dans les Ecosystèmes’for financial support, European Project: 223681,EC:FP7:HEALTH,FP7-HEALTH-2007-B,TB PAN-NET(2009), European Project: 278864,FP7/2007- 2013, Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), École pratique des hautes études (EPHE), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF), Centre National de la Recherche Scientifique (CNRS)-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Université de Lille-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur de Lille, Universität Bern [Bern], Laboratoire Jean Alexandre Dieudonné (JAD), Université Côte d'Azur (UCA)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS), THALES-ALCATEL, and Technical University of Denmark [Lyngby] (DTU)

Subjects
Tuberculosis, Lineage (genetic), MESH: Mutation, MESH: Mycobacterium tuberculosis, Genotype, MESH: Biological Evolution, MESH: Global Health, Biology, MESH: Genome, Bacterial, Global Health, Genetic analysis, Mycobacterium tuberculosis, MESH: Genotype, Evolution, Molecular, Phylogenetics, Tuberculosis, Multidrug-Resistant, Genetics, Global health, medicine, Humans, MESH: Phylogeny, MESH: Evolution, Molecular, MESH: Tuberculosis, Multidrug-Resistant, Phylogeny, MESH: Humans, Ecology, Population size, medicine.disease, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Biological Evolution, 3. Good health, Mycobacterium tuberculosis/classification/genetics/isolation & purification, Evolutionary biology, Mutation, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Tuberculosis, Multidrug-Resistant/epidemiology/microbiology, Genome, Bacterial, purl.org/pe-repo/ocde/ford#1.06.07 [https]
Abstract

International audience; Mycobacterium tuberculosis strains of the Beijing lineage are globally distributed and are associated with the massive spread of multidrug-resistant (MDR) tuberculosis in Eurasia. Here we reconstructed the biogeographical structure and evolutionary history of this lineage by genetic analysis of 4,987 isolates from 99 countries and whole-genome sequencing of 110 representative isolates. We show that this lineage initially originated in the Far East, from where it radiated worldwide in several waves. We detected successive increases in population size for this pathogen over the last 200 years, practically coinciding with the Industrial Revolution, the First World War and HIV epidemics. Two MDR clones of this lineage started to spread throughout central Asia and Russia concomitantly with the collapse of the public health system in the former Soviet Union. Mutations identified in genes putatively under positive selection and associated with virulence might have favored the expansion of the most successful branches of the lineage.

Published
2015
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